deseq_contrasts: Obtain pairwise contrasts with shrunken log2FC from a DESeq...

In mirvie/mirmisc: Non-Modeling Helper Functions For Mirvie R Coders

Description

Obtain pairwise contrasts with shrunken log2FC from a DESeq object.

Usage

deseq_contrasts(ddsx, compr, alpha = 0.05, shrink = TRUE)

Arguments

ddsx	A DESeq object, output from deseq_wide().
compr	A character vector for pairwise comparisons of interest, eg., c("4", "1") from draw 4 with samples from draw 1.
alpha	A number. The significance level.
shrink	A flag. DESeq2::lfcShrink() the result? Default yes.

Value

A dataframe.

See Also

Other Arkady: check_sample_descs(), collapse_tech_reps(), deseq_pairs(), deseq_wide(), fgsea_basic(), plot_cond_paired_pearson(), plot_down(), plot_metrics_global(), plot_var_mean_ratio(), prep_gsea_input_gene_set(), prep_gsea_input_lfc(), prep_rd_input(), reconcile_names()

Examples

rs_genes <- arrow::read_feather(
  system.file("extdata", "rs_genes_draw_3_4.feather", package = "mirmisc")
)
rs_meta <- arrow::read_feather(
  system.file("extdata", "rs_meta_draw_3_4.feather", package = "mirmisc")
)
ddsx <- deseq_wide(rs_genes, rs_meta, compvar = "meta_draw")
deseq_contrasts(ddsx, compr = c("4", "3"))

mirvie/mirmisc documentation built on Dec. 21, 2021, 7 p.m.