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Compare scRNA-seq data to reference data.

Usage

clustify(input, ...)

# S3 method for default
clustify(
  input,
  ref_mat,
  metadata = NULL,
  cluster_col = NULL,
  query_genes = NULL,
  n_genes = 1000,
  per_cell = FALSE,
  n_perm = 0,
  compute_method = "spearman",
  pseudobulk_method = "mean",
  verbose = TRUE,
  lookuptable = NULL,
  rm0 = FALSE,
  obj_out = TRUE,
  seurat_out = TRUE,
  vec_out = FALSE,
  rename_prefix = NULL,
  threshold = "auto",
  low_threshold_cell = 0,
  exclude_genes = c(),
  if_log = TRUE,
  organism = "hsapiens",
  plot_name = NULL,
  rds_name = NULL,
  expand_unassigned = FALSE,
  ...
)

# S3 method for Seurat
clustify(
  input,
  ref_mat,
  cluster_col = NULL,
  query_genes = NULL,
  n_genes = 1000,
  per_cell = FALSE,
  n_perm = 0,
  compute_method = "spearman",
  pseudobulk_method = "mean",
  use_var_genes = TRUE,
  dr = "umap",
  seurat_out = TRUE,
  obj_out = TRUE,
  vec_out = FALSE,
  threshold = "auto",
  verbose = TRUE,
  rm0 = FALSE,
  rename_prefix = NULL,
  exclude_genes = c(),
  metadata = NULL,
  organism = "hsapiens",
  plot_name = NULL,
  rds_name = NULL,
  expand_unassigned = FALSE,
  ...
)

# S3 method for SingleCellExperiment
clustify(
  input,
  ref_mat,
  cluster_col = NULL,
  query_genes = NULL,
  per_cell = FALSE,
  n_perm = 0,
  compute_method = "spearman",
  pseudobulk_method = "mean",
  use_var_genes = TRUE,
  dr = "umap",
  seurat_out = TRUE,
  obj_out = TRUE,
  vec_out = FALSE,
  threshold = "auto",
  verbose = TRUE,
  rm0 = FALSE,
  rename_prefix = NULL,
  exclude_genes = c(),
  metadata = NULL,
  organism = "hsapiens",
  plot_name = NULL,
  rds_name = NULL,
  expand_unassigned = FALSE,
  ...
)

Arguments

input

single-cell expression matrix or Seurat object

...

additional arguments to pass to compute_method function

ref_mat

reference expression matrix

metadata

cell cluster assignments, supplied as a vector or data.frame. If data.frame is supplied then cluster_col needs to be set. Not required if running correlation per cell.

cluster_col

column in metadata that contains cluster ids per cell. Will default to first column of metadata if not supplied. Not required if running correlation per cell.

query_genes

A vector of genes of interest to compare. If NULL, then common genes between the expr_mat and ref_mat will be used for comparision.

n_genes

number of genes limit for Seurat variable genes, by default 1000, set to 0 to use all variable genes (generally not recommended)

per_cell

if true run per cell, otherwise per cluster.

n_perm

number of permutations, set to 0 by default

compute_method

method(s) for computing similarity scores

pseudobulk_method

method used for summarizing clusters, options are mean (default), median, truncate (10% truncated mean), or trimean, max, min

verbose

whether to report certain variables chosen and steps

lookuptable

if not supplied, will look in built-in table for object parsing

rm0

consider 0 as missing data, recommended for per_cell

obj_out

whether to output object instead of cor matrix

seurat_out

output cor matrix or called seurat object (deprecated, use obj_out instead)

vec_out

only output a result vector in the same order as metadata

rename_prefix

prefix to add to type and r column names

threshold

identity calling minimum correlation score threshold, only used when obj_out = TRUE

low_threshold_cell

option to remove clusters with too few cells

exclude_genes

a vector of gene names to throw out of query

if_log

input data is natural log, averaging will be done on unlogged data

organism

for GO term analysis, organism name: human - 'hsapiens', mouse - 'mmusculus'

plot_name

name for saved pdf, if NULL then no file is written (default)

rds_name

name for saved rds of rank_diff, if NULL then no file is written (default)

expand_unassigned

test all ref clusters for unassigned results

use_var_genes

if providing a seurat object, use the variable genes (stored in seurat_object@var.genes) as the query_genes.

dr

stored dimension reduction

Value

single cell object with identity assigned in metadata, or matrix of correlation values, clusters from input as row names, cell types from ref_mat as column names

Examples

# Annotate a matrix and metadata
clustify(
    input = pbmc_matrix_small,
    metadata = pbmc_meta,
    ref_mat = cbmc_ref,
    query_genes = pbmc_vargenes,
    cluster_col = "classified",
    verbose = TRUE
)
#> using # of genes: 599
#> similarity computation completed, matrix of 9 x 13, preparing output
#>                      B CD14+ Mono CD16+ Mono     CD34+     CD4 T
#> B            0.9093577  0.5347126  0.5908755 0.6248639 0.6411407
#> CD14+ Mono   0.5279272  0.9145428  0.8919954 0.5103056 0.4636934
#> CD8 T        0.5791953  0.4853982  0.5498177 0.5663773 0.7657468
#> DC           0.6088123  0.7415535  0.7520484 0.5694074 0.4951613
#> FCGR3A+ Mono 0.5380921  0.8429769  0.9294914 0.5331927 0.4857454
#> Memory CD4 T 0.6268758  0.5373744  0.5866177 0.6265186 0.8610826
#> NK           0.5042912  0.4399003  0.5092065 0.5350808 0.6755032
#> Naive CD4 T  0.6443057  0.5213433  0.5625255 0.6480900 0.8891488
#> Platelet     0.1456751  0.2571662  0.2867421 0.2455947 0.1422081
#>                  CD8 T        DC     Eryth Memory CD4 T        Mk
#> B            0.6269530 0.6036723 0.4817829    0.4803367 0.2241017
#> CD14+ Mono   0.4381450 0.7643448 0.4559350    0.4553454 0.4227047
#> CD8 T        0.7692801 0.5187820 0.5007841    0.6323214 0.2961827
#> DC           0.4789794 0.8493399 0.4470039    0.4764929 0.2948557
#> FCGR3A+ Mono 0.4643569 0.7235944 0.4604308    0.4614474 0.3937726
#> Memory CD4 T 0.8347482 0.5541873 0.5395170    0.7128879 0.2635539
#> NK           0.6926741 0.4817286 0.4578726    0.5665250 0.2783269
#> Naive CD4 T  0.8707703 0.5419174 0.5528441    0.7277404 0.2668581
#> Platelet     0.1208273 0.1898078 0.3068445    0.1457308 0.7319575
#>              Naive CD4 T        NK      pDCs
#> B              0.5407149 0.5484213 0.5823418
#> CD14+ Mono     0.4564707 0.5917870 0.4738376
#> CD8 T          0.6036230 0.8257838 0.4536589
#> DC             0.4475783 0.5643991 0.6825388
#> FCGR3A+ Mono   0.4574654 0.6028156 0.4797367
#> Memory CD4 T   0.6871755 0.6999959 0.4696025
#> NK             0.5505877 0.8940904 0.4185162
#> Naive CD4 T    0.6967073 0.6880495 0.4631464
#> Platelet       0.1609963 0.1396979 0.2152614

# Annotate using a different method
clustify(
    input = pbmc_matrix_small,
    metadata = pbmc_meta,
    ref_mat = cbmc_ref,
    query_genes = pbmc_vargenes,
    cluster_col = "classified",
    compute_method = "cosine"
)
#> using # of genes: 599
#> similarity computation completed, matrix of 9 x 13, preparing output
#>                      B CD14+ Mono CD16+ Mono     CD34+     CD4 T
#> B            0.9669867  0.7149343  0.7720125 0.8004738 0.7635724
#> CD14+ Mono   0.7527223  0.9627275  0.9460084 0.7577338 0.7096110
#> CD8 T        0.7510063  0.7070527  0.7467587 0.7677927 0.8562280
#> DC           0.8230905  0.8842235  0.9086642 0.8037140 0.7246647
#> FCGR3A+ Mono 0.7590829  0.9172636  0.9762851 0.7746692 0.7286717
#> Memory CD4 T 0.7865337  0.7486511  0.7797697 0.8075621 0.9318837
#> NK           0.6784059  0.6671718  0.7107553 0.7238537 0.7777913
#> Naive CD4 T  0.7986227  0.7404425  0.7704809 0.8194404 0.9493149
#> Platelet     0.5463488  0.5932935  0.6068613 0.5953661 0.5558004
#>                  CD8 T        DC     Eryth Memory CD4 T        Mk
#> B            0.7657181 0.8062767 0.6514282    0.7123319 0.6594086
#> CD14+ Mono   0.7061112 0.8919577 0.6951238    0.7557225 0.7911713
#> CD8 T        0.8674614 0.7351337 0.6826181    0.8232194 0.7188642
#> DC           0.7260570 0.9560634 0.6874076    0.7519049 0.7448677
#> FCGR3A+ Mono 0.7274581 0.8800476 0.6880012    0.7601400 0.7722167
#> Memory CD4 T 0.9235744 0.7594695 0.7101214    0.8855087 0.7122113
#> NK           0.7973584 0.6864934 0.6500106    0.7578212 0.6960715
#> Naive CD4 T  0.9444251 0.7508430 0.7181980    0.8877208 0.7125300
#> Platelet     0.5516889 0.5730797 0.5898023    0.5655621 0.8775257
#>              Naive CD4 T        NK      pDCs
#> B              0.7494337 0.6957714 0.7863873
#> CD14+ Mono     0.7542713 0.7675894 0.7495702
#> CD8 T          0.8123971 0.9018633 0.7085898
#> DC             0.7491931 0.7595771 0.8503681
#> FCGR3A+ Mono   0.7561998 0.7776798 0.7477358
#> Memory CD4 T   0.8731255 0.8102022 0.7241459
#> NK             0.7544227 0.9480188 0.6812692
#> Naive CD4 T    0.8847456 0.8097839 0.7246787
#> Platelet       0.5455913 0.5569351 0.5756617

# Annotate a Seurat object
clustify(
    s_small3,
    cbmc_ref,
    cluster_col = "RNA_snn_res.1",
    obj_out = TRUE,
    per_cell = FALSE,
    dr = "tsne"
)
#> object data retrieval complete, moving to similarity computation
#> using # of genes: 19
#> similarity computation completed, matrix of 3 x 13, preparing output
#> using threshold of 0.55
#> seurat not loaded, returning cor_mat instead
#>            B CD14+ Mono CD16+ Mono       CD34+     CD4 T      CD8 T
#> 0 -0.4449320 -0.2097411 -0.2220272 -0.07199298 0.2887232 0.37971905
#> 1  0.4283876  0.7219124  0.7316084  0.53439673 0.3472936 0.29497641
#> 2  0.6248032  0.4460352  0.4973646  0.38956668 0.1769981 0.03275902
#>           DC      Eryth Memory CD4 T          Mk Naive CD4 T         NK
#> 0 -0.3168822  0.4203598    0.1987308  0.62044762 -0.08992247 0.08688022
#> 1  0.5865428  0.1736468    0.5311026  0.02027349  0.51050337 0.54297685
#> 2  0.5146717 -0.1716881    0.1094072 -0.45488507  0.23853307 0.32921643
#>        pDCs
#> 0 0.1134067
#> 1 0.4370882
#> 2 0.3758960

# Annotate (and return) a Seurat object per-cell
clustify(
    input = s_small3,
    ref_mat = cbmc_ref,
    cluster_col = "RNA_snn_res.1",
    obj_out = TRUE,
    per_cell = TRUE,
    dr = "tsne"
)
#> object data retrieval complete, moving to similarity computation
#> using # of genes: 19
#> similarity computation completed, matrix of 80 x 13, preparing output
#> using threshold of NA
#> seurat not loaded, returning cor_mat instead
#>                          B  CD14+ Mono  CD16+ Mono         CD34+
#> ATGCCAGAACGACT          NA          NA          NA            NA
#> CATGGCCTGTGCAT  0.03131121  0.09393364  0.03131121 -0.0156624783
#> GAACCTGATGAACC  0.02635231  0.44798934  0.44798934  0.0790916384
#> TGACTGGATTCTCA  0.28987545  0.31622777  0.31622777  0.4218220716
#> AGTCAGACTGCACA          NA          NA          NA            NA
#> TCTGATACACGTGT          NA          NA          NA            NA
#> TGGTATCTAAACAG  0.00000000  0.12909944  0.12909944  0.3013642443
#> GCAGCTCTGTTTCT  0.30123204  0.38729833  0.34426519  0.3444162792
#> GATATAACACGCAT          NA          NA          NA            NA
#> AATGTTGACAGTCA  0.00000000  0.12909944  0.12909944  0.3013642443
#> AGGTCATGAGTGTC  0.44426166 -0.03619910  0.02961744  0.0888913276
#> AGAGATGATCTCGC  0.43780788  0.38123720  0.45256545  0.4798314923
#> GGGTAACTCTAGTG  0.56817622  0.01244182  0.08709271  0.1203236639
#> CATGAGACACGGGA  0.53311399  0.34882767  0.44426166  0.4148261957
#> TACGCCACTCCGAA  0.20732211  0.17112301  0.29617444  0.2963044255
#> CTAAACCTGTGCAT  0.53311399  0.34882767  0.44426166  0.4148261957
#> GTAAGCACTCATTC  0.53311399  0.34882767  0.44426166  0.4148261957
#> TTGGTACTGAATCC  0.16709137 -0.01519012  0.03452301 -0.1920321845
#> CATCATACGGAGCA  0.38729833  0.30123204  0.38729833  0.3874683141
#> TACATCACGCTAAC  0.38569627  0.25298357  0.38569627  0.3609709916
#> TTACCATGAATCGC  0.54822542  0.56479646  0.50679780  0.4835342775
#> ATAGGAGAAACAGA  0.70897476  0.66220212  0.67081813  0.6501787611
#> GCGCACGACTTTAC  0.57170106  0.63522340  0.60070039  0.6009640307
#> ACTCGCACGAAAGT  0.57170106  0.63522340  0.60070039  0.6009640307
#> ATTACCTGCCTTAT  0.37910456  0.54527052  0.46895726  0.4900968692
#> CCCAACTGCAATCG  0.57232349  0.63038530  0.59720712  0.5974692276
#> AAATTCGAATCACG  0.38389588  0.49436952  0.41289521  0.4365623763
#> CCATCCGATTCGCC  0.57170106  0.63522340  0.60070039  0.6009640307
#> TCCACTCTGAGCTT  0.37877761  0.71328250  0.70098453  0.4847528410
#> CATCAGGATGCACA  0.52808777  0.79519008  0.79824850  0.6843675909
#> CTAAACCTCTGACA  0.38648971  0.45418696  0.43449321  0.5455098318
#> GATAGAGAAGGGTG  0.38729833  0.30123204  0.38729833  0.3874683141
#> CTAACGGAACCGAT  0.12909944  0.21516574  0.17213259  0.2152601745
#> AGATATACCCGTAA  0.30604692  0.43109835  0.36857264  0.4016571101
#> TACTCTGAATCGAC  0.30604692  0.43109835  0.36857264  0.4016571101
#> GCGCATCTTGCTCC  0.27642948  0.40148091  0.30933775  0.3423962250
#> GTTGACGATATCGG  0.25132752  0.43498994  0.38251496  0.5166909137
#> ACAGGTACTGGTGT  0.12909944  0.21516574  0.17213259  0.2152601745
#> GGCATATGCTTATC  0.12909944  0.21516574  0.17213259  0.2152601745
#> CATTACACCAACTG  0.01244182  0.17003814  0.19077450  0.3194800731
#> TAGGGACTGAACTC  0.09872481  0.25339369  0.22048542  0.3720266675
#> GCTCCATGAGAAGT  0.48523079  0.32763446  0.41057990  0.4107600939
#> TACAATGATGCTAG          NA          NA          NA            NA
#> CTTCATGACCGAAT  0.12909944  0.21516574  0.17213259  0.2152601745
#> CTGCCAACAGGAGC  0.38729833  0.30123204  0.38729833  0.3874683141
#> TTGCATTGAGCTAC  0.38729833  0.30123204  0.38729833  0.3874683141
#> AAGCAAGAGCTTAG  0.12909944  0.21516574  0.17213259  0.2152601745
#> CGGCACGAACTCAG  0.12909944  0.21516574  0.17213259  0.2152601745
#> GGTGGAGATTACTC  0.09872481  0.25339369  0.22048542  0.3720266675
#> GGCCGATGTACTCT          NA          NA          NA            NA
#> CGTAGCCTGTATGC  0.57998659  0.63246156  0.60898591  0.6092531897
#> TGAGCTGAATGCTG  0.39572399  0.75086091  0.80159476  0.5836952851
#> CCTATAACGAGACG  0.50349655  0.49691489  0.53311399  0.5333479659
#> ATAAGTTGGTACGT  0.46400662  0.47058828  0.46400662  0.4642102666
#> AAGCGACTTTGACG  0.30648388  0.70528219  0.70282047  0.4322211082
#> ACCAGTGAATACCG  0.60435175  0.51572991  0.56619512  0.5664436176
#> ATTGCACTTGCTTT  0.50952655  0.81225781  0.82078545  0.5865326293
#> CTAGGTGATGGTTG  0.49827856  0.74062313  0.76893441  0.5245550569
#> GCACTAGACCTTTA  0.23061371  0.55374910  0.58274843  0.3246587292
#> CATGCGCTAGTCAC  0.08492927  0.50095960  0.55880997  0.3829651415
#> TTGAGGACTACGCA  0.45637786  0.29556978  0.36464931  0.3489480724
#> ATACCACTCTAAGC  0.64687344  0.44518667  0.44026748  0.3494157534
#> CATATAGACTAAGC  0.59924986  0.49029534  0.48916040  0.4655308205
#> TTTAGCTGTACTCT  0.70897476  0.66220212  0.67081813  0.6501787611
#> GACATTCTCCACCT  0.64687344  0.44518667  0.44026748  0.3494157534
#> ACGTGATGCCATGA  0.74687208  0.64955238  0.61334040  0.5434180874
#> ATTGTAGATTCCCG  0.71266734  0.65112439  0.66589470  0.6427903661
#> GATAGAGATCACGA  0.58731304  0.56694381  0.58957629  0.5705889918
#> AATGCGTGGACGGA  0.70405133  0.66712556  0.66835642  0.6477159628
#> GCGTAAACACGGTT  0.42560359  0.29735504  0.31551413  0.3497158359
#> ATTCAGCTCATTGG -0.38390303 -0.36760526 -0.36851069 -0.2241926923
#> GGCATATGGGGAGT -0.23100622 -0.09966801 -0.12761231 -0.0009318855
#> ATCATCTGACACCA -0.54852438 -0.55232040 -0.54093235 -0.4941734325
#> GTCATACTTCGCCT -0.54821729 -0.52963366 -0.52777529 -0.3950756052
#> TTACGTACGTTCAG -0.60147674 -0.57730611 -0.57637647 -0.4557232615
#> GAGTTGTGGTAGCT -0.40140656 -0.33636383 -0.35123074 -0.2323974148
#> GACGCTCTCTCTCG -0.43668863 -0.44158424 -0.48858212 -0.3599854390
#> AGTCTTACTTCGGA -0.39931430 -0.31620828 -0.32026223 -0.2185025336
#> GGAACACTTCAGAC -0.52492894 -0.44281715 -0.45259237 -0.4513240771
#> CTTGATTGATCTTC  0.19190801  0.30548622  0.30059061  0.4114119302
#>                       CD4 T       CD8 T          DC        Eryth
#> ATGCCAGAACGACT           NA          NA          NA           NA
#> CATGGCCTGTGCAT  0.156556073  0.21927470 -0.01572473  0.250489716
#> GAACCTGATGAACC  0.184466197  0.14500134 -0.02646866  0.105409255
#> TGACTGGATTCTCA  0.316227766  0.31636655  0.39702990  0.131761569
#> AGTCAGACTGCACA           NA          NA          NA           NA
#> TCTGATACACGTGT           NA          NA          NA           NA
#> TGGTATCTAAACAG  0.258198890  0.25831221  0.12966942  0.258198890
#> GCAGCTCTGTTTCT  0.387298335  0.38746831  0.30256199  0.344265186
#> GATATAACACGCAT           NA          NA          NA           NA
#> AATGTTGACAGTCA  0.258198890  0.25831221  0.12966942  0.258198890
#> AGGTCATGAGTGTC -0.134923911 -0.12016791  0.07437051 -0.204031280
#> AGAGATGATCTCGC  0.336964493  0.33711238  0.42244764  0.113141363
#> GGGTAACTCTAGTG -0.186627226 -0.17218731  0.20619631 -0.356665365
#> CATGAGACACGGGA  0.102015640  0.10206041  0.53546771 -0.144796392
#> TACGCCACTCCGAA  0.190867972  0.13169086  0.35697847 -0.055944061
#> CTAAACCTGTGCAT  0.102015640  0.10206041  0.53546771 -0.144796392
#> GTAAGCACTCATTC  0.102015640  0.10206041  0.53546771 -0.144796392
#> TTGGTACTGAATCC -0.451560984 -0.47248207 -0.12552506 -0.553749097
#> CATCATACGGAGCA  0.172132593  0.17220814  0.38900827  0.043033148
#> TACATCACGCTAAC  0.141007237  0.09128002  0.51236659 -0.194921769
#> TTACCATGAATCGC  0.447418223  0.44761459  0.52429252  0.327278145
#> ATAGGAGAAACAGA  0.476342419  0.47655148  0.69108792  0.286790138
#> GCGCACGACTTTAC  0.564796461  0.56504434  0.54787181  0.491607677
#> ACTCGCACGAAAGT  0.564796461  0.56504434  0.54787181  0.491607677
#> ATTACCTGCCTTAT  0.670818135  0.67111255  0.31401848  0.626507212
#> CCCAACTGCAATCG  0.555734405  0.55597831  0.54569124  0.485230787
#> AAATTCGAATCACG  0.470893871  0.33018484  0.35923747  0.562034620
#> CCATCCGATTCGCC  0.564796461  0.56504434  0.54787181  0.491607677
#> TCCACTCTGAGCTT  0.391075580  0.36171912  0.41503628  0.322206924
#> CATCAGGATGCACA  0.469977727  0.34779337  0.60516951  0.387400295
#> CTAAACCTCTGACA  0.476342419  0.51841905  0.43641152  0.327408484
#> GATAGAGAAGGGTG  0.172132593  0.17220814  0.38900827  0.043033148
#> CTAACGGAACCGAT  0.301232038  0.30136424  0.17289256  0.215165741
#> AGATATACCCGTAA  0.496914892  0.49713298  0.34045169  0.401480906
#> TACTCTGAATCGAC  0.496914892  0.49713298  0.34045169  0.401480906
#> GCGCATCTTGCTCC  0.467297448  0.46750254  0.28095528  0.431098350
#> GTTGACGATATCGG  0.571701063  0.57195197  0.36062449  0.490226757
#> ACAGGTACTGGTGT  0.301232038  0.30136424  0.17289256  0.215165741
#> GGCATATGCTTATC  0.301232038  0.30136424  0.17289256  0.215165741
#> CATTACACCAACTG  0.402285353  0.35267281  0.24160376  0.219805399
#> TAGGGACTGAACTC  0.408062560  0.40824165  0.22145887  0.342246018
#> GCTCCATGAGAAGT  0.091239977 -0.05808729  0.48737310 -0.020736358
#> TACAATGATGCTAG           NA          NA          NA           NA
#> CTTCATGACCGAAT  0.301232038  0.30136424  0.17289256  0.215165741
#> CTGCCAACAGGAGC  0.172132593  0.17220814  0.38900827  0.043033148
#> TTGCATTGAGCTAC  0.172132593  0.17220814  0.38900827  0.043033148
#> AAGCAAGAGCTTAG  0.301232038  0.30136424  0.17289256  0.215165741
#> CGGCACGAACTCAG  0.301232038  0.30136424  0.17289256  0.215165741
#> GGTGGAGATTACTC  0.408062560  0.40824165  0.22145887  0.342246018
#> GGCCGATGTACTCT           NA          NA          NA           NA
#> CGTAGCCTGTATGC  0.553749097  0.55399213  0.55896795  0.469512950
#> TGAGCTGAATGCTG  0.391665287  0.32839204  0.56359368  0.158289598
#> CCTATAACGAGACG  0.398190079  0.39836484  0.50571950  0.269847822
#> ATAAGTTGGTACGT  0.381735943  0.38190348  0.43300166  0.325791883
#> AAGCGACTTTGACG  0.322485048  0.28568461  0.36099763  0.253556946
#> ACCAGTGAATACCG  0.308945600  0.18347848  0.60701998  0.182167127
#> ATTGCACTTGCTTT  0.413590591  0.38177942  0.57601581  0.215322936
#> CTAGGTGATGGTTG  0.302364489  0.27190759  0.54483907  0.120039835
#> GCACTAGACCTTTA  0.161567692  0.12640968  0.27601643  0.100807192
#> CATGCGCTAGTCAC  0.193244857  0.15454060  0.24973124  0.076313256
#> TTGAGGACTACGCA  0.096258358  0.03852024  0.64720966 -0.255933987
#> ATACCACTCTAAGC  0.108222173  0.08612360  0.67443395 -0.142656501
#> CATATAGACTAAGC  0.447167509  0.42806127  0.56313714  0.172511323
#> TTTAGCTGTACTCT  0.476342419  0.47655148  0.69108792  0.286790138
#> GACATTCTCCACCT  0.108222173  0.08612360  0.67443395 -0.142656501
#> ACGTGATGCCATGA  0.380225786  0.36341085  0.76267237  0.157295786
#> ATTGTAGATTCCCG  0.452956098  0.45315489  0.69603310  0.251095228
#> GATAGAGATCACGA  0.355330050  0.40643144  0.61718494  0.446991623
#> AATGCGTGGACGGA  0.488651008  0.48886547  0.68614275  0.304022164
#> GCGTAAACACGGTT  0.061286917  0.09991881  0.60189557 -0.232663298
#> ATTCAGCTCATTGG  0.061569354  0.07246632 -0.39878470  0.164788566
#> GGCATATGGGGAGT  0.287826301  0.24881343 -0.14501633  0.436862573
#> ATCATCTGACACCA -0.156585679 -0.09684090 -0.56524404  0.074971325
#> GTCATACTTCGCCT -0.070617821 -0.05019784 -0.53757171 -0.007433455
#> TTACGTACGTTCAG -0.086456470  0.05394275 -0.61020161  0.049270892
#> GAGTTGTGGTAGCT  0.109643459  0.23239741 -0.35651457  0.241587282
#> GACGCTCTCTCTCG -0.014686837  0.03330478 -0.54138667 -0.025457185
#> AGTCTTACTTCGGA -0.004053952  0.14195060 -0.32218518  0.228034815
#> GGAACACTTCAGAC -0.055718715  0.06552267 -0.46588170  0.155425888
#> CTTGATTGATCTTC  0.488582124  0.55932431  0.18341256  0.361296200
#>                Memory CD4 T          Mk Naive CD4 T          NK
#> ATGCCAGAACGACT           NA          NA          NA          NA
#> CATGGCCTGTGCAT  0.162793072  0.31311215  0.13949369  0.06262243
#> GAACCTGATGAACC  0.548043144  0.23717082  0.19077734  0.36893239
#> TGACTGGATTCTCA  0.258798151 -0.21081851  0.42558021  0.44798934
#> AGTCAGACTGCACA           NA          NA          NA          NA
#> TCTGATACACGTGT           NA          NA          NA          NA
#> TGGTATCTAAACAG  0.348036386 -0.17213259  0.11982234  0.25819889
#> GCAGCTCTGTTTCT  0.397755870  0.25819889  0.38343149  0.30123204
#> GATATAACACGCAT           NA          NA          NA          NA
#> AATGTTGACAGTCA  0.348036386 -0.17213259  0.11982234  0.25819889
#> AGGTCATGAGTGTC -0.252842573 -0.33237354  0.08796522 -0.10201564
#> AGAGATGATCTCGC  0.166242832 -0.13527772  0.41776119  0.40829274
#> GGGTAACTCTAGTG -0.318645377 -0.48523079  0.17552572 -0.08709271
#> CATGAGACACGGGA -0.252842573 -0.27313865  0.38484782  0.22377624
#> TACGCCACTCCGAA -0.252842573 -0.09543399  0.08796522  0.19415880
#> CTAAACCTGTGCAT -0.252842573 -0.27313865  0.38484782  0.22377624
#> GTAAGCACTCATTC -0.252842573 -0.27313865  0.38484782  0.22377624
#> TTGGTACTGAATCC -0.114874767 -0.58551027 -0.08766741 -0.13809204
#> CATCATACGGAGCA -0.174018193 -0.08606630  0.28757362  0.21516574
#> TACATCACGCTAAC -0.318645377 -0.25713084  0.22171669  0.21980540
#> TTACCATGAATCGC  0.445937465  0.19332886  0.65212250  0.45984651
#> ATAGGAGAAACAGA  0.251001602  0.09354528  0.72657229  0.51696076
#> GCGCACGACTTTAC  0.445937465  0.31070710  0.67826892  0.53027345
#> ACTCGCACGAAAGT  0.445937465  0.31070710  0.67826892  0.53027345
#> ATTACCTGCCTTAT  0.820554811  0.43941665  0.60456298  0.59573574
#> CCCAACTGCAATCG  0.431249382  0.30275083  0.67900737  0.53085078
#> AAATTCGAATCACG  0.445937465  0.28723145  0.41680471  0.38941956
#> CCATCCGATTCGCC  0.445937465  0.31070710  0.67826892  0.53027345
#> TCCACTCTGAGCTT  0.507253771  0.17217164  0.54788352  0.55586843
#> CATCAGGATGCACA  0.468205999 -0.05199320  0.59611538  0.63615206
#> CTAAACCTCTGACA  0.189851070  0.17847455  0.67859110  0.53419279
#> GATAGAGAAGGGTG -0.174018193 -0.08606630  0.28757362  0.21516574
#> CTAACGGAACCGAT  0.248597419  0.12909944  0.33550255  0.38729833
#> AGATATACCCGTAA  0.463861562  0.27642948  0.52046087  0.50349655
#> TACTCTGAATCGAC  0.463861562  0.27642948  0.52046087  0.50349655
#> GCGCATCTTGCTCC  0.498080857  0.30604692  0.55344782  0.53311399
#> GTTGACGATATCGG  0.596710598  0.12290192  0.50831718  0.58274843
#> ACAGGTACTGGTGT  0.248597419  0.12909944  0.33550255  0.38729833
#> GGCATATGCTTATC  0.248597419  0.12909944  0.33550255  0.38729833
#> CATTACACCAACTG  0.268332949 -0.03732545  0.18476391  0.43546353
#> TAGGGACTGAACTC  0.429642266 -0.01974496  0.33903261  0.47387910
#> GCTCCATGAGAAGT -0.318645377 -0.30689810  0.22171669  0.17003814
#> TACAATGATGCTAG           NA          NA          NA          NA
#> CTTCATGACCGAAT  0.248597419  0.12909944  0.33550255  0.38729833
#> CTGCCAACAGGAGC -0.174018193 -0.08606630  0.28757362  0.21516574
#> TTGCATTGAGCTAC -0.174018193 -0.08606630  0.28757362  0.21516574
#> AAGCAAGAGCTTAG  0.248597419  0.12909944  0.33550255  0.38729833
#> CGGCACGAACTCAG  0.248597419  0.12909944  0.33550255  0.38729833
#> GGTGGAGATTACTC  0.429642266 -0.01974496  0.33903261  0.47387910
#> GGCCGATGTACTCT           NA          NA          NA          NA
#> CGTAGCCTGTATGC  0.406050393  0.28585053  0.66904077  0.52198793
#> TGAGCTGAATGCTG  0.429660319 -0.10146769  0.52550324  0.63620242
#> CCTATAACGAGACG  0.140679326  0.11188812  0.48380869  0.37186346
#> ATAAGTTGGTACGT  0.222425421  0.17112301  0.52779130  0.41135339
#> AAGCGACTTTGACG  0.497025834  0.11939332  0.48118278  0.53542365
#> ACCAGTGAATACCG -0.051195794 -0.11570074  0.42360536  0.32863934
#> ATTGCACTTGCTTT  0.447063321  0.02984674  0.68859139  0.68434319
#> CTAGGTGATGGTTG  0.332989700 -0.03737089  0.58397625  0.53904680
#> GCACTAGACCTTTA  0.264052417 -0.01519012  0.35220767  0.42532350
#> CATGCGCTAGTCAC  0.307885817 -0.23632492  0.27280733  0.51696076
#> TTGAGGACTACGCA -0.215233028 -0.48129179  0.18036415  0.17552995
#> ATACCACTCTAAGC -0.093778008 -0.26563624  0.41639148  0.20906556
#> CATATAGACTAAGC  0.009834647  0.10895452  0.54354705  0.40971439
#> TTTAGCTGTACTCT  0.251001602  0.09354528  0.72657229  0.51696076
#> GACATTCTCCACCT -0.093778008 -0.26563624  0.41639148  0.20906556
#> ACGTGATGCCATGA  0.221613127 -0.01131624  0.63774561  0.40964802
#> ATTGTAGATTCCCG  0.216871072  0.06031209  0.71697605  0.50342132
#> GATAGAGATCACGA  0.254299429  0.05997609  0.64530781  0.39946340
#> AATGCGTGGACGGA  0.283710026  0.11323902  0.73205586  0.52188420
#> GCGTAAACACGGTT -0.101624685 -0.21904398  0.28567822  0.19748007
#> ATTCAGCTCATTGG -0.203469249  0.60573379 -0.32370946 -0.25261544
#> GGCATATGGGGAGT  0.152821279  0.39960350 -0.16287946  0.05216270
#> ATCATCTGACACCA -0.211067964  0.52005426 -0.53746937 -0.41376579
#> GTCATACTTCGCCT -0.260873812  0.52777529 -0.44914350 -0.37538947
#> TTACGTACGTTCAG -0.146612397  0.54012053 -0.41830262 -0.36162975
#> GAGTTGTGGTAGCT  0.001073555  0.57051766 -0.23699046 -0.13566055
#> GACGCTCTCTCTCG -0.160638212  0.60509770 -0.32170196 -0.29079938
#> AGTCTTACTTCGGA  0.037470726  0.36890966 -0.18625042 -0.23816970
#> GGAACACTTCAGAC -0.028235126  0.46432262 -0.38595542 -0.30791921
#> CTTGATTGATCTTC  0.535649250  0.52480966  0.43457028  0.38283689
#>                       pDCs
#> ATGCCAGAACGACT          NA
#> CATGGCCTGTGCAT  0.21956404
#> GAACCTGATGAACC  0.15839201
#> TGACTGGATTCTCA  0.26398668
#> AGTCAGACTGCACA          NA
#> TCTGATACACGTGT          NA
#> TGGTATCTAAACAG  0.08621769
#> GCAGCTCTGTTTCT  0.34487075
#> GATATAACACGCAT          NA
#> AATGTTGACAGTCA  0.08621769
#> AGGTCATGAGTGTC  0.14834771
#> AGAGATGATCTCGC  0.54945445
#> GGGTAACTCTAGTG  0.25342857
#> CATGAGACACGGGA  0.50438220
#> TACGCCACTCCGAA  0.23735633
#> CTAAACCTGTGCAT  0.50438220
#> GTAAGCACTCATTC  0.50438220
#> TTGGTACTGAATCC -0.14940175
#> CATCATACGGAGCA  0.38797960
#> TACATCACGCTAAC  0.38637471
#> TTACCATGAATCGC  0.52843951
#> ATAGGAGAAACAGA  0.69295952
#> GCGCACGACTTTAC  0.57547339
#> ACTCGCACGAAAGT  0.57547339
#> ATTACCTGCCTTAT  0.50800591
#> CCCAACTGCAATCG  0.56917565
#> AAATTCGAATCACG  0.43437174
#> CCATCCGATTCGCC  0.57547339
#> TCCACTCTGAGCTT  0.38190780
#> CATCAGGATGCACA  0.58008007
#> CTAAACCTCTGACA  0.29099368
#> GATAGAGAAGGGTG  0.38797960
#> CTAACGGAACCGAT  0.04310884
#> AGATATACCCGTAA  0.27032249
#> TACTCTGAATCGAC  0.27032249
#> GCGCATCTTGCTCC  0.18131386
#> GTTGACGATATCGG  0.26975315
#> ACAGGTACTGGTGT  0.04310884
#> GGCATATGCTTATC  0.04310884
#> CATTACACCAACTG  0.02908197
#> TAGGGACTGAACTC  0.09230524
#> GCTCCATGAGAAGT  0.51101172
#> TACAATGATGCTAG          NA
#> CTTCATGACCGAAT  0.04310884
#> CTGCCAACAGGAGC  0.38797960
#> TTGCATTGAGCTAC  0.38797960
#> AAGCAAGAGCTTAG  0.04310884
#> CGGCACGAACTCAG  0.04310884
#> GGTGGAGATTACTC  0.09230524
#> GGCCGATGTACTCT          NA
#> CGTAGCCTGTATGC  0.58654019
#> TGAGCTGAATGCTG  0.42793039
#> CCTATAACGAGACG  0.53405175
#> ATAAGTTGGTACGT  0.43185666
#> AAGCGACTTTGACG  0.31318811
#> ACCAGTGAATACCG  0.65103671
#> ATTGCACTTGCTTT  0.46770961
#> CTAGGTGATGGTTG  0.48781061
#> GCACTAGACCTTTA  0.20473573
#> CATGCGCTAGTCAC  0.09001076
#> TTGAGGACTACGCA  0.22915754
#> ATACCACTCTAAGC  0.33755722
#> CATATAGACTAAGC  0.65374010
#> TTTAGCTGTACTCT  0.69295952
#> GACATTCTCCACCT  0.33755722
#> ACGTGATGCCATGA  0.52939816
#> ATTGTAGATTCCCG  0.69419255
#> GATAGAGATCACGA  0.52032924
#> AATGCGTGGACGGA  0.69049348
#> GCGTAAACACGGTT  0.26718074
#> ATTCAGCTCATTGG  0.15600819
#> GGCATATGGGGAGT  0.23514503
#> ATCATCTGACACCA -0.05513906
#> GTCATACTTCGCCT -0.04840245
#> TTACGTACGTTCAG -0.10057767
#> GAGTTGTGGTAGCT  0.04467918
#> GACGCTCTCTCTCG  0.06767829
#> AGTCTTACTTCGGA -0.04771773
#> GGAACACTTCAGAC -0.02154330
#> CTTGATTGATCTTC  0.49630746