heatMapRegion {ORFik}R Documentation

Create coverage heatmaps of specified region

Description

Simplified input space for easier abstraction of coverage heatmaps
Pick your transcript region and plot directly
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,
  plot.ext = ".pdf",
  acceptedLengths = 21:75,
  upstream = c(50, 30),
  downstream = c(29, 69),
  shifting = c("5prime", "3prime"),
  longestPerGene = FALSE
)

Arguments

df

an ORFik experiment

region

a character, default "TIS", can be any combination of the set: c("TSS", "TIS", "TTS", "TES"), which are: Transcription start site (5' end of mrna), Translation initation site (5' end of CDS), Translation termination site (3' end of CDS), Transcription end site (3' end of 3' UTRs)

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.

plot.ext

a character, default ".pdf", alternative ".png"

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 NULL (no shifting of reads). If NULL, will use first index of 'upstream' and 'downstream' argument.

longestPerGene

logical (TRUE), return only longest valid transcript per gene. NOTE: This is by priority longest cds isoform, if equal then pick longest total transcript. So if transcript is shorter but cds is longer, it will still be the one returned.

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")

[Package ORFik version 1.12.13 Index]