man/BamTallyParam-class.Rd
 b22faf0d  \name{BamTallyParam-class} \Rdversion{1.1} \docType{class} \alias{BamTallyParam-class} \alias{coerce,BamTallyParam,list-method} \alias{as.list,BamTallyParam-method} \alias{BamTallyParam} \title{Class \code{"BamTallyParam"}} \description{ A \code{BamTallyParam} object stores parameters for \code{\link{bam_tally}}. The function of the same name serves as its constructor. } \usage{  0c270851  BamTallyParam(genome, which = GRanges(),  4d5cc806  desired_read_group = NULL,  b22faf0d  minimum_mapq = 0L, concordant_only = FALSE, unique_only = FALSE,  df903e03  primary_only = FALSE, ignore_duplicates = FALSE,  c3db7e3b  min_depth = 0L, variant_strand = 0L, variant_pct = 0,  b22faf0d  ignore_query_Ns = FALSE,  c3db7e3b  indels = FALSE, min_softclip = 0L, max_softclip = 0L,  f053c5f3  exon_iit = NULL, IIT_BPPARAM = NULL, xs = FALSE, read_pos = FALSE, min_base_quality = 0L, noncovered = FALSE, nm = FALSE)  b22faf0d  } \arguments{  16509777  \item{genome}{A \code{GmapGenome} object, or something coercible to one.}  c0871141  \item{which}{A \code{IntegerRangesList} or something coercible to  b22faf0d  one that limits the tally to that range or set of ranges. By default, the entire genome is processed. }  4d5cc806  \item{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.}  b22faf0d  \item{minimum_mapq}{Minimum mapping quality for a read to be counted at all.} \item{concordant_only}{Consider only what gnsap calls \dQuote{concordant} alignments. } \item{unique_only}{Consider only the uniquly mapped reads.} \item{primary_only}{Consider only primary pairs.}  df903e03  \item{ignore_duplicates}{Whether to ignore the reads flagged as PCR/optical duplicates. }  b22faf0d  \item{min_depth}{The minimum number of reads overlapping a position for it to be counted.} \item{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.}  c3db7e3b  \item{variant_pct}{The minimum alternate allele fraction for a variant to be reported for a strand.}  b22faf0d  \item{ignore_query_Ns}{Whether to ignore the N base pairs when counting. Can save a lot of resources when processing low quality data.}  4d5cc806  \item{indels}{Whether to return indel counts. The \code{ref} and \code{alt} columns in the returned \code{VRanges} conform to VCF conventions; i.e., the first base upstream is included. The range always spans the sequence in \code{ref}; so e.g. a deletion extends one nt upstream of the actual deleted sequence. }  c3db7e3b  \item{min_softclip, max_softclip}{ Minimum and maximum length of soft clips that are  17db5e75  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. }  c78be696  \item{exon_iit}{An object which indicates the exons to be used for tallying codons (a character value indicating an existing .iit file, a \code{GRangesList} of exons by gene or a \code{TxDb} object from which to make such a \code{GRangesList}) or \code{NULL} indicating no codon-level tallying should be done.} \item{IIT_BPPARAM}{A \code{BiocParallelParam} object to use when generating the iit file from an R object. Ignored if \code{exon_iit} is a character vector or \code{NULL}  f5e63d36  }  f053c5f3  \item{xs}{Whether to tabulate reads by XS tag, the aligner's best guess about the strand of transcription. } \item{read_pos}{Whether to tabulate by read position. } \item{min_base_quality}{Minimum base quality cutoff. Calls of lower quality are not counted, except in the total raw depth. } \item{noncovered}{ Whether to report zero tallies, where there is no coverage. } \item{nm}{ Whether to tally by NM tag, the number of mismatches for a read. }  b22faf0d  } \seealso{ \code{\link{bam_tally}} }