computeBamStats: Computes the BAM statistics

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

Computes the BAM statistics

Description

Computes the BAM statistics.

Usage

computeBamStats(input, htmlFile, param, gff, resultList = NULL)

getPosErrorFromBam(bamFile, param)

ezPosSpecErrorRate(bam, ReferenceGenome, nMaxReads = 1e+05)

getStatsFromBam(param, bamFile, sm, gff = NULL, repeatsGff = NULL, nReads = NA)

getStatsFromBamParallel(
  seqLengths,
  param,
  bamFile,
  sm,
  gff = NULL,
  repeatsGff = NULL,
  mc.cores = ezThreads(),
  nReads = NA
)

getStatsFromBamSingleChrom(
  chrom,
  param,
  bamFile,
  sm,
  gff = NULL,
  repeatsGff = NULL
)

getTargetTypeCounts(param, gff, rr, seqid = NULL, repeatsGff = NULL)

getJunctionPlotsFromBam(bamFile, param)

Arguments

input	a list, file path or an object of the class EzDataset containing the input.
htmlFile	a character, ending with .html, representing the file path of an html file.
param	a list of parameters: ezRef@refBuild a character containing the path of the reference build. seqNames the sequence names to select. posErrorRates a logical indicating whether to call getPosErrorFromBam(). saveImage a logical indicating whether to save the image.
gff	an annotation data.frame in gtf or gff format.
resultList	a list of results.

Functions

• getPosErrorFromBam: Gets the error positions from the BAM file.

• ezPosSpecErrorRate: Calculates the specific error rates for getPosErrorFromBam().

• getStatsFromBam: Gets the result statistics from the BAM file.

• getStatsFromBamParallel: Gets parallel by chromosome statistics for getStatsFromBam() if the logical param$splitByChrom is true.

• getStatsFromBamSingleChrom: Gets the statistics of a single chromosome for getStatsFromBam().

• getTargetTypeCounts: Gets the counts of the target types for getStatsFromBam().

• getJunctionPlotsFromBam: Gets the junction results from the BAM file.

Author(s)

Rehrauer, Hubert

Schmid, Peter

See Also

plotBamStat

uzh/ezRun documentation built on April 14, 2024, 5:09 a.m.