Extract genes, i.e. "features", based on the top loadings of principal components formed from the bulk expression data set
Arguments
- mat
Expression matrix. Rownames are genes, colnames are single cell cluster name, and values are average single cell expression (log transformed).
- pcs
Precalculated pcs if available, will skip over processing on mat.
- n_pcs
Number of PCs to selected gene loadings from. See the explore_PCA_corr.Rmd vignette for details.
- percentile
Select the percentile of absolute values of PCA loadings to select genes from. E.g. 0.999 would select the top point 1 percent of genes with the largest loadings.
- if_log
whether the data is already log transformed
Examples
feature_select_PCA(
cbmc_ref,
if_log = FALSE
)
#> [1] "HLA-DRA" "CST3" "HLA-DPB1" "HLA-DRB1"
#> [5] "HLA-DPA1" "TYROBP" "IL32" "HLA-DQB1"
#> [9] "HLA-DRB5" "IFI30" "RP11-1143G9.4" "FCN1"
#> [13] "TRAC" "SPI1" "MS4A6A" "LGALS2"
#> [17] "CD68" "CSTA" "CEBPD" "CLEC12A"
#> [21] "HBG1" "HBA2" "KLRB1" "IL32"
#> [25] "HBM" "AHSP" "CD7" "IL7R"
#> [29] "TRBC2" "CD3D" "CA1" "EVL"
#> [33] "IFITM1" "GYPA" "ALAS2" "CD3G"
#> [37] "MT2A" "FYB" "LINC00861" "GIMAP4"
#> [41] "HBG2" "HBG1" "HBA1" "HLA-DPB1"
#> [45] "IGJ" "HLA-DQB1" "HLA-DQA1" "ITM2C"
#> [49] "PLD4" "FCER1A" "ALOX5AP" "IRF7"
#> [53] "IRF8" "HBD" "SERPINF1" "MZB1"
#> [57] "LILRA4" "CA2" "SPIB" "STOM"
#> [61] "PPBP" "GZMB" "PF4" "CCL5"
#> [65] "PTGDS" "GNG11" "SDPR" "HIST1H2AC"
#> [69] "CLIC3" "TUBB1" "PTCRA" "ACRBP"
#> [73] "C12orf75" "GZMH" "GP9" "MYL9"
#> [77] "CLEC1B" "TREML1" "CMTM5" "MAP3K7CL"
#> [81] "IGHM" "TCL1A" "CD79A" "FABP4"
#> [85] "RHOC" "MS4A1" "IGHD" "TXN"
#> [89] "PRSS57" "MPO" "MATK" "IGFBP7"
#> [93] "TXK" "SERPINB6" "NDUFS3" "UQCRFS1"
#> [97] "RASSF1" "STOML2" "ILF2" "MACF1"
#> [101] "GZMB" "GNLY" "NKG7" "GNG11"
#> [105] "FCGR3A" "HOPX" "PRF1" "KLRF1"
#> [109] "GZMH" "CMC1" "SPON2" "FABP4"
#> [113] "KLRD1" "NGFRAP1" "CCL4" "FGFBP2"
#> [117] "CD160" "KLRC1" "EGFL7" "TTC38"
#> [121] "HBG2" "CD7" "IGHM" "CD69"
#> [125] "CLIC3" "HOPX" "CD79B" "MS4A1"
#> [129] "SPINK2" "IGHD" "CD36" "YBX3"
#> [133] "C1QTNF4" "KIAA0125" "VPREB3" "AVP"
#> [137] "BASP1" "LAT2" "PARP1" "RCSD1"
#> [141] "HBG1" "IGJ" "TCL1A" "CEBPB"
#> [145] "IGLC2" "CD79A" "CD79B" "ID2"
#> [149] "IGLC3" "MS4A1" "SPINK2" "C1QTNF4"
#> [153] "VPREB3" "LINC00926" "RP5-887A10.1" "ANKRD28"
#> [157] "AVP" "FCRLA" "IGLC7" "ZFP36L1"
#> [161] "KLRB1" "IGHM" "SERPINF1" "MS4A1"
#> [165] "TOB1" "IGHD" "TRDC" "CD63"
#> [169] "LEF1" "BST2" "S100B" "CD8B"
#> [173] "ACTN1" "LAT2" "OXNAD1" "C1orf228"
#> [177] "LDLRAP1" "RP4-594I10.3" "NELL2" "PAG1"
#> [181] "FCGR3A" "FCER1A" "SERPINA1" "GPR183"
#> [185] "CLEC10A" "TOB1" "RP11-290F20.3" "CD1C"
#> [189] "C5AR1" "PPP1R14A" "RGS1" "BASP1"
#> [193] "C1QA" "CDKN1C" "ENHO" "APOBEC3A"
#> [197] "ITGB7" "CD1E" "NDRG2" "FCGR2B"