countTable_regions: Make a list of count matrices from experiment

In ORFik: Open Reading Frames in Genomics

Description

Make a list of count matrices from experiment

Usage

countTable_regions(
  df,
  out.dir = dirname(df$filepath[1]),
  longestPerGene = TRUE,
  geneOrTxNames = "tx",
  regions = c("mrna", "leaders", "cds", "trailers"),
  type = "count",
  lib.type = "ofst",
  weight = "score",
  BPPARAM = bpparam()
)

Arguments

df	an ORFik experiment
out.dir	optional output directory, default: dirname(df$filepath[1]). Will make a folder called "QC_STATS" with all results in this directory.
longestPerGene	a logical (default TRUE), if FALSE all transcript isoforms per gene.
geneOrTxNames	a character vector (default "tx"), should row names keep trancript names ("tx") or change to gene names ("gene")
regions	a character vector, default: c("mrna", "leaders", "cds", "trailers"), make raw count matrices of whole regions specified.
type	default: "count" (raw counts matrix), alternative is "fpkm", "log2fpkm" or "log10fpkm"
lib.type	a character(default: "default"), load files in experiment or some precomputed variant, either "ofst", "bedo", "bedoc" or "pshifted". These are made with ORFik:::convertLibs() or shiftFootprintsByExperiment(). Can also be custom user made folders inside the experiments bam folder.
weight	numeric or character, a column to score overlaps by. Default "score", will check for a metacolumn called "score" in libraries. If not found, will not use weights.
BPPARAM	how many cores/threads to use? default: bpparam()

Value

a list of data.table, 1 data.table per region. The regions will be the names the list elements.

See Also

Other countTable: countTable()

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