make_voom: Convert count data to voom

In latlio/tidyde: Tidy Differential Expression

Description

'make_voom()' is a wrapper function for 'voom()'

Usage

make_voom(.dge, design_matrix, .f = limma::voom, ...)

Arguments

.dge	a 'list' or a 'DGElist' object
design_matrix	a design matrix with rows corresponding to samples and columns to coefficients to be estimated
.f	limma::voom
...	additional arguments passed to '.f'

Details

Please refer to voom for more information.

Value

a 'list' with the following components:

E	a numeric matrix of normalized expression values on the log2 scale
weights	numeric matrix of inverse variance weights
design	design matrix
lib.size	numeric vector of total normalized library sizes
genes	dataframe of gene annotation extracted from 'counts'

Examples

counts <- readr::read_delim("data/GSE60450_Lactation-GenewiseCounts.txt", delim = "\t")
meta <- readr::read_delim("data/SampleInfo_Corrected.txt", delim = "\t") %>%
  mutate(FileName = stringr::str_replace(FileName, "\\.", "-"))

id <- as.character(counts$EntrezGeneID)
check_sample_names(counts, c(1,2), meta, FileName) %>%
  purrr::pluck("mod_count") %>%
  filter_genes(., id, "edgeR") %>%
  make_voom(., my_design)

latlio/tidyde documentation built on Dec. 21, 2021, 9:40 a.m.