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A helper function to create a ScanBamParam object

strandedScanBamParam.Rd

helper function to create ScanBamParam object with appropriate strandedness information

Usage

strandedScanBamParam(
  locus_granges,
  library_strandedness,
  quality_threshold = 20L
)

Arguments

locus_granges

a granges object for a given gene (or some other feature on only one strand)

library_strandedness

one of c("reverse", "same", "unstranded")

quality_threshold

quality threshold above which reads will be considered. 20l is default, which is chosen b/c it is the default for HTSeq

Value

a ScanBamParam object with certain configured options, as well as some reasonable defaults, to filter a bam file for reads of interest based on the strandedness (protocol) of the library prep.

See also

ScanBamParam