scFrac

Using a SVR method to deconvolute the cell fraction in a mixture sample using single cell seq data

install:

devtools::install_github(“shenxiaotianCNS/scFrac”)

usage:

scfrac(mixture,seuratobjext,nPerm)

example using built in data:

YY is the mixture matrix, with sample in colum and gene in row

scFrac::YY[1:10,1:10]
 	TCGA-DD-A4NG-01A TCGA-G3-AAV4-01A TCGA-2Y-A9H1-01A TCGA-BC-A10Y-01A TCGA-K7-AAU7-01A TCGA-BC-A10W-01A TCGA-DD-AACV-01A TCGA-DD-AAD3-01A TCGA-DD-A39X-11A
Saa3      0.000000000       0.00000000        0.0000000       0.00000000      0.193145155       0.06098851       0.00000000      0.000000000      0.000000000
Slpi      0.000000000       0.01298560        0.0000000       0.00000000      0.007151308       0.00000000       0.00000000      0.000000000      0.000000000
Cfd       0.992363695       1.47831339        2.0442644       0.95705156      1.869666411       0.86207485       2.84978438      1.686785001      1.044961450
Gsn       0.000000000       0.00000000        0.0000000       0.00000000      0.000000000       0.00000000       0.00000000      0.000000000      0.000000000
Mgp       1.392656043       0.92825171        0.4713262       0.71804958      1.459199734       1.98783478       1.09027908      1.561597709      0.233239536
C3        2.817509427       2.55078471        1.2341101       2.57167794      4.036040339       3.62839474       2.52398312      2.178161108      1.467522500
Clu       0.000000000       0.00000000        0.0000000       0.00000000      0.000000000       0.00000000       0.00000000      0.000000000      0.000000000
Apoe      0.007685404       0.00000000        0.0000000       0.01545603      0.045854259       0.02200552       0.04186160      0.003619704      0.001381904
Spp1      6.314781981       6.89906641        7.6036875       6.42415254      6.695148838       6.33296179       6.46912497      6.382021747      5.771885926
Gpx3      0.000000000       0.04264948        0.1331687       0.24864715      0.136112062       0.18798788       0.09950746      0.227252876      0.000000000
     TCGA-DD-A1EI-01A
Saa3      0.640680779
Slpi      0.000000000
Cfd       1.794992695
Gsn       0.000000000
Mgp       1.586118993
C3        3.427686108
Clu       0.000000000
Apoe      0.004095529
Spp1      6.936311336
Gpx3      0.287640770

Fibroblast_ is a seurat object

scFrac::fibroblasts_
An object of class Seurat 
13851 features across 200 samples within 1 assay 
Active assay: RNA (13851 features, 2000 variable features)
 2 dimensional reductions calculated: pca, umap

running: using nPerm=5

scfrac(fibroblasts_[,1:200],YY[,1:20],nPerm = 5)
Calculating cluster iCAF
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=01s  
Calculating cluster myCAF
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=01s  
Calculating cluster apCAF
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=01s  
[1] 1
[1] 2
[1] 3
[1] 4
[1] 5
                      myCAF      iCAF        apCAF
TCGA-DD-A4NG-01A 0.09992375 0.8937604 0.0063158924
TCGA-G3-AAV4-01A 0.09720270 0.8974404 0.0053569342
TCGA-2Y-A9H1-01A 0.08198760 0.9149265 0.0030859354
TCGA-BC-A10Y-01A 0.09793974 0.8926296 0.0094306161
TCGA-K7-AAU7-01A 0.10658258 0.8874751 0.0059422883

release

0.1.0

only SVR was added, the elastic network regression and xgboost regression will be added soon