countTable_regions: Make a list of count matrices from experiment

In JokingHero/ORFik: Open Reading Frames in Genomics

Make a list of count matrices from experiment

Description

By default will make count tables over mRNA, leaders, cds and trailers for all libraries in experiment. Saved as "qs" or "rds" format files.

Usage

countTable_regions(
  df,
  out.dir = libFolder(df),
  longestPerGene = FALSE,
  geneOrTxNames = "tx",
  regions = c("mrna", "leaders", "cds", "trailers"),
  type = "count",
  lib.type = "ofst",
  weight = "score",
  rel.dir = "QC_STATS",
  forceRemake = FALSE,
  library.names = bamVarName(df),
  format = "qs",
  BPPARAM = bpparam()
)

Arguments

df	an ORFik experiment
out.dir	character, output directory, default: resFolder(df). Will make a folder within this called "QC_STATS" with all results in this directory. Warning: If you assign not default path, you will have a hazzle to load files later. Much easier to load count tables, statistics, ++ later with default. Update resFolder of df instead if needed.
longestPerGene	a logical (default FALSE), if FALSE all transcript isoforms per gene. Ignored if "region" is not a character of either: "mRNA","tx", "cds", "leaders" or "trailers".
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. Can also be a custom GRangesList of for example uORFs or a subset of cds etc.
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.
rel.dir	relative output directory for out.dir, default: "QC_STATS". For pshifted, write "pshifted".
forceRemake	logical, default FALSE. If TRUE, will not look for existing file count table files.
library.names	character, default: bamVarName(df). Names to load libraries as to environment and names to display in plots.
format	character, default "qs", alternative: "rds". Which format to save summarizedExperiment.
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()

Examples

##Make experiment
df <- ORFik.template.experiment()
## Create count tables for all default regions
# countTable_regions(df)
## Pshifted reads (first create pshiftead libs)
# countTable_regions(df, lib.type = "pshifted", rel.dir = "pshifted")

JokingHero/ORFik documentation built on June 9, 2025, 8:46 p.m.