drop_uninformative_genes: drop_uninformative_genes

Description Usage Arguments Value Examples

View source: R/drop_uninformative_genes.r

Description

drop_uninformative_genes drops genes from an SCT expression matrix if they do not significantly vary between any celltypes. Makes this decision based on use of an ANOVA (implemented with Limma). If the F-statistic for variation amongst type2 annotations is less than a strict p-threshold, then the gene is dropped.

Usage

1

Arguments

exp

Expression matrix with gene names as rownames.

level2annot

Array of cell types, with each sequentially corresponding a column in the expression matrix

Value

exp Expression matrix with gene names as rownames.

Examples

1
2
3
4
5
library(ewceData)
cortex_mrna <- cortex_mrna()
cortex_mrna$exp <- cortex_mrna$exp[1:300, ] 
exp2 <- drop_uninformative_genes(exp = cortex_mrna$exp, 
    level2annot = cortex_mrna$annot$level2class)

NathanSkene/EWCE documentation built on June 19, 2021, 5:40 a.m.