top_counts: Get a count matrix of top genes

In HuntsmanCancerInstitute/hciR: RNA-seq workflows at HCI

Get a count matrix of top genes

Description

Join DESeq results to rlog or other counts, mainly for plotting gene heatmaps.

Usage

top_counts(
  res,
  rld,
  by = "id",
  filter = TRUE,
  col_names,
  row_names = "gene_name",
  collapse,
  ...
)

Arguments

res	an annotated DESeq2 results file
rld	rlog or other counts in DESeqTransform object
by	join count rownames by this column number in results, default id
filter	filter the results using top_genes
col_names	optionally replace sample IDs with another column in colData(rld)
row_names	a column name in results to use as row names, default gene_name
collapse	collapse replicates and group by column means in colData(rld)
...	additional options passed to top_genes

Value

A tibble with colData attribute

Author(s)

Chris Stubben

Examples

x <- top_counts(pasilla$results, pasilla$rlog)
x

HuntsmanCancerInstitute/hciR documentation built on Aug. 20, 2024, 12:22 a.m.