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_colneeds 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