heatMapRegion: Create coverage heatmaps of specified region

In ORFik: Open Reading Frames in Genomics

Description

Simplified input space for easier abstraction of coverage heatmaps
Pick your region and plot
Input CAGE file if you use TSS and want improved 5' annotation.

Usage

heatMapRegion(
  df,
  region = "TIS",
  outdir = "default",
  scores = c("transcriptNormalized", "sum"),
  type = "ofst",
  cage = NULL,
  format = ".png",
  acceptedLengths = 21:75,
  upstream = c(50, 30),
  downstream = c(29, 69),
  shifting = c("5prime", "3prime")
)

Arguments

df	an ORFik experiment
region	a character, default "TIS", can be any combination of the set: c("TSS", "TIS", "TTS"), which are: Transcription start site (5' end of mrna), Translation initation site (5' end of CDS), Translation termination site (3' end of CDS)
outdir	a character path, default: "default", saves to: paste0(dirname(df$filepath[1]), "/QC_STATS/heatmaps/"), a created folder within the ORFik experiment data folder for plots. Change if you want custom location.
scores	character vector, default c("transcriptNormalized", "sum"), either of zscore, transcriptNormalized, sum, mean, median, .. see ?coverageScorings for info and more alternatives.
type	character, default: "ofst". Type of library: either "default", usually bam format (the one you gave to experiment), "pshifted" pshifted reads, "ofst", "bed", "bedo" optimized bed, or "wig"
cage	a character path to library file or a GRanges, GAlignments preloaded file of CAGE data. Only used if "TSS" is defined as region, to redefine 5' leaders.
format	a character, default ".png", alternative ".pdf"
acceptedLengths	an integer vector (NULL), the read lengths accepted. Default NULL, means all lengths accepted.
upstream	1 or 2 integers, default c(50, 30), how long upstream from 0 should window extend (first index is 5' end extension, second is 3' end extension). If only 1 shifting, only 1 value should be given, if two are given will use first.
downstream	1 or 2 integers, default c(29, 69), how long upstream from 0 should window extend (first index is 5' end extension, second is 3' end extension). If only 1 shifting, only 1 value should be given, if two are given will use first.
shifting	a character, default c("5prime", "3prime"), can also be either or NULL (no shifting of reads)

Value

invisible(NULL), plots are saved

See Also

Other heatmaps: coverageHeatMap(), heatMapL(), heatMap_single()

Examples

# Toy example, will not give logical output, but shows how it works
df <- ORFik.template.experiment()[3,] # Only third library
#heatMapRegion(df, "TIS", outdir = "default")
#
# Do also TSS, add cage for specific TSS
# heatMapRegion(df, c("TSS", "TIS"), cage = "path/to/cage.bed")

# Do on pshifted reads instead of original files
remove.experiments(df) # Remove loaded experiment first
# heatMapRegion(df, "TIS", type = "pshifted")

ORFik documentation built on March 27, 2021, 6 p.m.