Class "BamTallyParam"

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Description

A BamTallyParam object stores parameters for bam_tally. The function of the same name serves as its constructor.

Usage

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  BamTallyParam(genome, which = GRanges(),
                desired_read_group = NULL,
                minimum_mapq = 0L,
                concordant_only = FALSE, unique_only = FALSE,
                primary_only = FALSE, ignore_duplicates = FALSE,
                min_depth = 0L, variant_strand = 0L,
                ignore_query_Ns = FALSE,
                indels = FALSE, include_soft_clips = 0L,
                exon_iit = NULL, IIT_BPPARAM = NULL,
                xs = FALSE, read_pos = FALSE,
                min_base_quality = 0L, noncovered = FALSE, nm = FALSE)

Arguments

genome

A GmapGenome object, or something coercible to one.

which

A RangesList or something coercible to one that limits the tally to that range or set of ranges. By default, the entire genome is processed.

desired_read_group

The name of the read group to which to limit the tallying; if not NULL, must be a single, non-NA string.

minimum_mapq

Minimum mapping quality for a read to be counted at all.

concordant_only

Consider only what gnsap calls “concordant” alignments.

unique_only

Consider only the uniquly mapped reads.

primary_only

Consider only primary pairs.

ignore_duplicates

Whether to ignore the reads flagged as PCR/optical duplicates.

min_depth

The minimum number of reads overlapping a position for it to be counted.

variant_strand

The number of strands on which a variant must be seen for it to be counted. This means that a value of 0 will report reference alleles in addition to variants. A value of 1 will report only positions where a variant was seen on at least one strand, and 2 requires the variant be seen on both strands. Setting this to 1 is a good way to save resources.

ignore_query_Ns

Whether to ignore the N base pairs when counting. Can save a lot of resources when processing low quality data.

indels

Whether to return indel counts. The ref and alt columns in the returned VRanges conform to VCF conventions; i.e., the first base upstream is included. The range always spans the sequence in ref; so e.g. a deletion extends one nt upstream of the actual deleted sequence.

include_soft_clips

Maximum length of soft clips that are considered for counting. Soft-clipping is often useful (for GSNAP at least) during alignment, and it should be preserved in the output. However, soft clipping can preferentially occur in regions of discordance with the reference, and if those clipped regions are ignored during counting, the allele fraction is misestimated.

exon_iit

An object which indicates the exons to be used for tallying codons (a character value indicating an existing .iit file, a GRangesList of exons by gene or a TxDb object from which to make such a GRangesList) or NULL indicating no codon-level tallying should be done.

IIT_BPPARAM

A BiocParallelParam object to use when generating the iit file from an R object. Ignored if exon_iit is a character vector or NULL

xs

Whether to tabulate reads by XS tag, the aligner's best guess about the strand of transcription.

read_pos

Whether to tabulate by read position.

min_base_quality

Minimum base quality cutoff. Calls of lower quality are not counted, except in the total raw depth.

noncovered

Whether to report zero tallies, where there is no coverage.

nm

Whether to tally by NM tag, the number of mismatches for a read.

See Also

bam_tally