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wguo-research / scCancer

A package for automated processing of single cell RNA-seq data in cancer
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About ambient genes #29

Open evenDDDDD opened 3 years ago

evenDDDDD commented 3 years ago

Hi! I only have a filtered 10x matrix. When I ran "runScStatistics", I found that the step of "ambient genes" was skipped. I want to know if it is because there is no raw 10x matrix. Based on subsequent analysis, I found that environmental genes account for a large proportion of HVG's top, so I need to control environmental genes in first step. And why is the parameter of “bool.rmContamination “ unusual in “scAnnotation” step. Thanks! This is my code: bg.spec.genes<-list(igGenes=c('IGHA1','IGHA2','IGHG1','IGHG2','IGHG3','IGHG4','IGHD','IGHE','IGHM','IGLC1','IGLC2','IGLC3','IGLC4','IGLC5','IGLC6','IGLC7','IGKC','IGLL5','IGLL1'),HLAGenes=c('HLA-DRA','HLA-DRB5','HLA-DRB1','HLA-DQA1','HLA-DQB1','HLA-DQA2','HLA-DQB2','HLA-DPA1','HLA-DPB1'),HBGenes=c('HBB','HBD','HBG1','HBG2','HBE1','HBZ','HBM','HBA2','HBA1','HBQ1') ) dataPath="./BC_counts/" savePath="./runScStatistics_out/" sampleName="BC" authorName="LL" stat.results <- runScStatistics( dataPath = dataPath, savePath = savePath, sampleName = sampleName, authorName = authorName, bg.spec.genes = bg.spec.genes, bool.runSoupx = T )

dataPath <- "./BC_counts/"
statPath <- "./runScStatistics_out/" savePath <- "./runScAnnotation_out/" sampleName <- "BC"
authorName <- "LL"
anno.results <- runScAnnotation( dataPath = dataPath, statPath = statPath, savePath = savePath, authorName = authorName, sampleName = sampleName, geneSet.method = "average",
coor.names = c("UMAP_1", "UMAP_2"), bool.rmContamination = T, contamination.fraction=NULL )

wguo-research commented 3 years ago

The soupX will estimate a background distribution, so the raw data should be provided.