Plot metagene by regions

Usage

tx_plot_metageneRegions(
  txDT,
  geneAnnot,
  colVars,
  nBins_5UTR,
  nBins_CDS = NULL,
  nBins_3UTR = NULL,
  summ_fun = "mean",
  smooth = TRUE,
  spar = 0.5,
  nCores = 1,
  plot_type = "lineplot",
  normalize = FALSE
)

Arguments

txDT: data.table. A table as output by the tx_makeDT_coverage(), tx_makeDT_nucFreq() or tx_makeDT_covNucFreq() functions.
geneAnnot: GRanges. Gene annotation as loaded by tx_load_bed().
colVars: character. Names of columns for which values will be extracted
nBins_5UTR: integer. Number of bins into which allocate data on 5'UTR regions
nBins_CDS: integer. Number of bins into which allocate data on CDS regions
nBins_3UTR: integer. Number of bins into which allocate data on 3'UTR regions
summ_fun: character. Summarizing function either "sum" or "mean". Default: "mean"
smooth: logical. Set to FALSE for not smoothing line.
spar: numeric. Smoothing parameter, typically (but not necessarily) in (0,1].
nCores: integer. Number of cores to run the function with. Multicore capability not available in Windows OS. @param plot_type character. Type of plot to be output, either "lineplot" or "boxplot".
plot_type: character. Type of plot to be output, either "lineplot" or "boxplot".
normalize: logical. If set to TRUE, values are normalized so that the area bellow the curve approximates to 1 for each variable.

Value

ggplot