make_contrasts: Make contrasts

In latlio/tidyde: Tidy Differential Expression

Description

'make_contrasts()' computes estimated coefficients and standard errors for a given set of contrasts

Usage

make_contrasts(.fit, design_matrix, .condition1, .condition2)

Arguments

.fit	an MArrayLM object or list object. Must contain components 'coefficients' and 'stdev.unscaled'
design_matrix	a design matrix with rows corresponding to samples and columns to coefficients to be estimated
.condition1	the control
.condition2	the experimental
...	the names of the variables which you like to compare

Details

Please refer to contrasts.fit for more information.

Value

a 'list' object of the same class as .fit

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) %>%
  model_limma() %>%
  make_contrasts(Statuspregnant, Statusvirgin)

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