degSignature: Plot gene signature for each group and signature

In lpantano/DEGreport: Report of DEG analysis

Plot gene signature for each group and signature

Description

Given a list of genes beloging to a different classes, like markers, plot for each group, the expression values for all the samples.

Usage

degSignature(
  counts,
  signature,
  group = NULL,
  metadata = NULL,
  slot = 1,
  scale = FALSE
)

Arguments

counts	expression data. It accepts bcbioRNASeq, DESeqDataSet and SummarizedExperiment. As well, data.frame or matrix is supported, but it requires metadata in that case.
signature	data.frame with two columns: a) genes that match row.names of counts, b) label to classify the gene inside a group. Normally, cell tissue name.
group	character in metadata used to split data into different groups.
metadata	data frame with sample information. Rownames should match ma column names row number should be the same length than p-values vector.
slot	slotName in the case of SummarizedExperiment objects.
scale	Whether to scale or not the expression.

Value

ggplot plot.

Examples

data(humanGender)
data(geneInfo)
degSignature(humanGender, geneInfo, group = "group")

lpantano/DEGreport documentation built on Feb. 28, 2024, 12:01 a.m.