ezReadPairedAlignments: Reads paired alignments from bam

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

Reads paired alignments from bam

Description

Reads paired alignments from a bam file.

Usage

ezReadPairedAlignments(
  bamFile,
  seqname = NULL,
  start = NULL,
  end = NULL,
  strand = "*",
  tag = c("NH"),
  keepUnpaired = "both",
  fillGap = "N",
  minMapQuality = 0,
  keepMultiHits = TRUE
)

.ezMergeLeftRightAlignments(gaLeft, gaRight, fillGap = "N")

Arguments

bamFile	a character representing the bam file path.
seqname	an optional character vector to keep only the specified sequence names.
start	passed further to ezReadGappedAlignments().
end	passed further to ezReadGappedAlignments().
strand	a character specifying which strand to use (+, - or *).
tag	passed further to ezReadGappedAlignments().
keepUnpaired	a character indicating which aligned but unpaired reads to keep. Possible options: "none", "first", "second", "both".
fillGap	a character to fill into the gaps produced by ezMergeLeftRightAlignments().
minMapQuality	passed further to ezReadGappedAlignments().
keepMultiHits	passed further to ezReadGappedAlignments().
gaLeft	the left gapped alignments.
gaRight	the right gapped alignments.

Value

Returns an object of the class GAlignments.

Functions

• .ezMergeLeftRightAlignments: Merges left and right alignments and fills gaps with fillGap.

Author(s)

Rehrauer, Hubert

Schmid, Peter

See Also

ezReadGappedAlignments

Examples

bamFile <- system.file("extdata", "ex1.bam", package="Rsamtools", mustWork=TRUE)
ezReadPairedAlignments(bamFile)

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