make_comparison: Compare expression in two strains specified by contrats using...

In astrzalka/RNAseqHelper: RNA-seq Helper

Compare expression in two strains specified by contrats using edgeR package glmTreat

Description

Compare expression in two strains specified by contrats using edgeR package glmTreat

Usage

make_comparison(
  fit,
  contrast_comp,
  design,
  genes,
  plot_md = TRUE,
  plot_volcano = TRUE,
  complete_list = FALSE,
  fold_change = 1.5,
  toptags_print = 5
)

Arguments

fit	fit object made using edgeR package
contrast_comp	strains to compare, have to present in the design
design	design specifying which libraries belong to which strain
genes	data_frame containing genes data
plot_md	should md plot be shown? defaut TRUE
plot_volcano	should volcano plot be shown? default TRUE
complete_list	should it return complete list of genes or only those differentially expressed? default FALSE
fold_change	fold change used in glmTreat function
toptags_print	how many genes should be printed?

Value

result of topTags function for all or differentially expressed genes

astrzalka/RNAseqHelper documentation built on Oct. 24, 2023, 9:31 p.m.