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Gene expression in cells treated or not by a demethylating agent

Source: R/DAC_induction.R
DAC_induction.Rd

Plots a heatmap of normalised gene counts (log-transformed) in a selection of cells treated or not by 5-Aza-2'-Deoxycytidine (DAC), a demethylating agent.

Usage

DAC_induction(
  genes = NULL,
  multimapping = TRUE,
  include_CTP = FALSE,
  values_only = FALSE
)

Arguments

genes

character naming the selected genes. The default value, NULL, takes all CT specific genes.

multimapping

logical(1) defining whether to use multi-mapped gene expression dataset CTdata::DAC_treated_cells_multimapping or DAC_treated_cells. Default is TRUE.

include_CTP

logical(1) If TRUE, CTP genes are included. (FALSE by default).

values_only

logical(1). If TRUE, the function will return the gene normalised logcounts in all samples instead of the heatmap. Default is FALSE.

Value

A heatmap of selected genes in cells treated or not by a demethylating agent. If values_only is TRUE, gene normalised logcounts are returned instead.

Details

RNAseq data from cells treated or not with 5-aza downloaded from SRA. (SRA references and information about cell lines and DAC treatment are stored the colData of DAC_treated_cells). Data was processed using a standard RNAseq pipeline. hisat2 was used to align reads to grch38 genome. featurecounts was used to assign reads to genes. Note that -M parameter was used or not to allow or not counting multi-mapping reads.

Examples

DAC_induction(genes = c("MAGEA1", "MAGEA3", "MAGEA4", "MAGEA6", "CTAG1A"))
#> see ?CTdata and browseVignettes('CTdata') for documentation
#> loading from cache

DAC_induction(genes = c("MAGEA1", "MAGEA3", "MAGEA4", "MAGEA6", "CTAG1A",
    multimapping = FALSE))
#> see ?CTdata and browseVignettes('CTdata') for documentation
#> loading from cache
#> Warning: 1 out of 6 names invalid: FALSE.
#> See the manual page for valid types.