QC_gene: QC_gene removes genes that have TPM values < 1 in more than...

In Zouter/MPath: Mpath: a single-cell RNAseq data analysis algorithm that maps multi-branching single-cell trajectories revealing cell progression during development

Description

QC_gene removes genes that have TPM values < 1 in more than 95 percent of cells in each group

Usage

QC_gene(rpkmFile = "TPM_monocyte_Mar2015_noOutlier.txt",
  rpkmQCFile = "TPM_monocyte_Mar2015_noOutlier_geneQC0.05perGroup.txt",
  sampleFile = "monocyte_sample_Mar2015_noOutlier.txt", threshold = 0.05,
  method = "any")

Arguments

rpkmFile	a tab delimited file containing expression data (TPM, CPM, FPKM, etc), columns are cells and rows are genes.
rpkmQCFile	resulting file after QC
sampleFile	a tab delimited file containing sample annotations with two columns. The first column indicates SampleID, the second column indicates GroupID.
threshold	the cutoff of percentage of cells in which the given gene is not expressed.Default is 0.05.
method	keep genes whose rpkm values are not less than 1 in at least 5 percent of the cells in every group, method="any": keep genes whose rpkm values are not less than 1 in at least 5 percent of the cells in any group. Default is 'any'.

Examples

## Not run: 
QC_gene(rpkmFile = "TPM_MDP_CDP_preDC_Mar2015_noOutlier.txt",
        rpkmQCFile = "TPM_MDP_CDP_preDC_Mar2015_noOutlier_geneQC0.05anyGroup.txt",
        sampleFile = "sample_MDP_CDP_preDC_Mar2015_noOutlier.txt",
        threshold = 0.05,method = "any")

## End(Not run)

Zouter/MPath documentation built on May 4, 2019, 2:31 p.m.