SC_anova: SC_anova run ANOVA test to identify differentially expressed...

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

Description

SC_anova run ANOVA test to identify differentially expressed genes

Usage

SC_anova(inputfile, targetfile, iflog2, p_threshold, factor, baseName)

Arguments

inputfile	a tab delimied file containing expression values (TPM, CPM, FPKM, etc). Columns are cells and rows are genes.
targetfile	a tab delimited file indicating cell annoation with two columns. The first column indicates cell ID, the rest columns indicates cell annotations.
iflog2	a boolean value to indicate whether the expression values will be log2 transformed.
p_threshold	the cutoff of p values for DEGs.
factor	column name of targetfile, indicating which column will be used as cell annotation for comparison.
baseName	prefix name of resulting files.

Examples

## Not run: 
inputfile="GSE52529_fpkm_matrix_nooutliers_geneQC0.05anyGroup.txt";
targetfile="GSE52529_fpkm_matrix_nooutliers_ANOVA_p0.05_DEG_landmark_cluster.txt";
baseName="GSE52529_fpkm_matrix_nooutliers_ANOVA_p0.05_DEG_landmark_cluster";
SC_anova(inputfile = inputfile,
         targetfile = targetfile,
         iflog2 = TRUE,p_threshold=0.05,factor="landmark_cluster",
         baseName = baseName)

## End(Not run)

Zouter/MPath_gh documentation built on May 14, 2019, 8:58 a.m.