R: Parameters for scanning BAM files

ScanBamParam {Rsamtools}

R Documentation

Parameters for scanning BAM files

Description

Use ScanBamParam() to create a parameter object influencing what fields and which records are imported from a (binary) BAM file. Use of which requires that a BAM index file (<filename>.bai) exists.

Usage


# Constructor
ScanBamParam(flag = scanBamFlag(), simpleCigar = FALSE,
    reverseComplement = FALSE, tag = character(0),
    what = character(0), which)

# Constructor helpers
scanBamFlag(isPaired = NA, isProperPair = NA, isUnmappedQuery = NA, 
    hasUnmappedMate = NA, isMinusStrand = NA, isMateMinusStrand = NA, 
    isFirstMateRead = NA, isSecondMateRead = NA, isNotPrimaryRead = NA, 
    isValidVendorRead = NA, isDuplicate = NA) 
scanBamWhat()

# Accessors
bamFlag(object, asInteger=FALSE)
bamFlag(object) <- value
bamReverseComplement(object)
bamReverseComplement(object) <- value
bamSimpleCigar(object)
bamSimpleCigar(object) <- value
bamTag(object)
bamTag(object) <- value
bamWhat(object)
bamWhat(object) <- value
bamWhich(object)
bamWhich(object) <- value

## S4 method for signature 'ScanBamParam'
show(object)

# Flag utils
bamFlagAsBitMatrix(flag)
bamFlagAND(flag1, flag2)
bamFlagTest(flag, value)

Arguments

`flag`	For `ScanBamParam`, an integer(2) vector used to filter reads based on their 'flag' entry. This is most easily created with the `scanBamFlag()` helper function. For `bamFlagAsBitMatrix`, `bamFlagTest` an integer vector where each element represents a 'flag' entry.
`simpleCigar`	A logical(1) vector which, when TRUE, returns only those reads for which the cigar (run-length encoded representation of the alignment) is missing or contains only matches / mismatches (`'M'`).
`reverseComplement`	A logical(1) vector which, when TRUE, returns the sequence and quality scores of reads mapped to the minus strand in the reverse complement (sequence) and reverse (quality) of the read as stored in the BAM file.
`tag`	A character vector naming tags to be extracted. A tag is an optional field, with arbitrary information, stored with each record. Tags are identified by two-letter codes, so all elements of `tag` must have exactly 2 characters.
`what`	A character vector naming the fields to return. `scanBamWhat()` returns a vector of available fields. Fields are described on the `scanBam` help page.
`which`	A `GRanges`, `RangesList`, `RangedData`, or missing object, from which a `IRangesList` instance will be constructed. Names of the `IRangesList` correspond to reference sequences, and ranges to the regions on that reference sequence for which matches are desired. Because data types are coerced to `IRangesList`, `which` does not include strand information (use the `flag` argument instead). Only records with a read overlapping the specified ranges are returned. All ranges must have ends less than or equal to 536870912.
`isPaired`	A logical(1) indicating whether unpaired (FALSE), paired (TRUE), or any (NA) read should be returned.
`isProperPair`	A logical(1) indicating whether improperly paired (FALSE), properly paired (TRUE), or any (NA) read should be returned. A properly paired read is defined by the alignment algorithm and might, e.g., represent reads aligning to identical reference sequences and with a specified distance.
`isUnmappedQuery`	A logical(1) indicating whether unmapped (TRUE), mapped (FALSE), or any (NA) read should be returned.
`hasUnmappedMate`	A logical(1) indicating whether reads with mapped (FALSE), unmapped (TRUE), or any (NA) mate should be returned.
`isMinusStrand`	A logical(1) indicating whether reads aligned to the plus (FALSE), minus (TRUE), or any (NA) strand should be returned.
`isMateMinusStrand`	A logical(1) indicating whether mate reads aligned to the plus (FALSE), minus (TRUE), or any (NA) strand should be returned.
`isFirstMateRead`	A logical(1) indicating whether the first mate read should be returned (TRUE) or not (FALSE), or whether mate read number should be ignored (NA).
`isSecondMateRead`	A logical(1) indicating whether the second mate read should be returned (TRUE) or not (FALSE), or whether mate read number should be ignored (NA).
`isNotPrimaryRead`	A logical(1) indicating whether reads that are primary (FALSE), are not primary (TRUE) or whose primary status does not matter (NA) should be returned. A non-primary read might result when portions of a read aligns to multiple locations, e.g., when spanning splice junctions).
`isValidVendorRead`	A logical(1) indicating whether invalid (FALSE), valid (TRUE), or any (NA) read should be returned. A 'valid' read is one flagged by the vendor as passing quality control criteria.
`isDuplicate`	A logical(1) indicating that un-duplicated (FALSE), duplicated (TRUE), or any (NA) reads should be returned. 'Duplicated' reads may represent PCR or optical duplicates.
`object`	An instance of class `ScanBamParam`.
`value`	An instance of the corresponding slot, to be assigned to `object` or, for `bamFlagTest`, a `character(1)` name of the flag to test, e.g., “isUnmappedQuery”, from the arguments to `scanBamFlag`.
`asInteger`	logical(1) indicating whether ‘flag’ should be returned as an encoded integer vector (`TRUE`) or human-readable form (`FALSE`).
`flag1, flag2`	Integer vectors containing ‘flag’ entries.

Objects from the Class

Objects are created by calls of the form ScanBamParam().

Slots

flag: Object of class integer encoding flags to be kept when they have their '0' (keep0) or '1' (keep1) bit set.
simpleCigar: Object of class logical indicating, when TRUE, that only 'simple' cigars (empty or 'M') are returned.
reverseComplement: Object of class logical indicating, when TRUE, that reads on the minus strand are to be reverse complemented (sequence) and reversed (quality).
tag: Object of class character indicating what tags are to be returned.
what: Object of class character indicating what fields are to be returned.
which: Object of class RangesList indicating which reference sequence and coordinate reads must overlap.

Functions and methods

See 'Usage' for details on invocation.

Constructor:

ScanBamParam:: Returns a ScanBamParam object. The which argument to the constructor can be one of several different types, as documented above.

Accessors:

bamTag, bamTag<-: Returns or sets a character vector of tags to be extracted.
bamWhat, bamWhat<-: Returns or sets a character vector of fields to be extracted.
bamWhich, bamWhich<-: Returns or sets a RangesList of bounds on reads to be extracted. A length 0 RangesList represents all reads.
bamFlag, bamFlag<-: Returns or sets an integer(2) representation of reads flagged to be kept or excluded.
bamSimpleCigar, bamSimpleCigar<-: Returns or sets a logical(1) vector indicating whether reads without indels or clipping be kept.
bamReverseComplement, bamReverseComplement<-: Returns or sets a logical(1) vector indicating whether reads on the minus strand will be returned with sequence reverse complemented and quality reversed.

Methods:

show: Compactly display the object.

Author(s)

Martin Morgan

Examples

## defaults
p0 <- ScanBamParam()

## subset of reads based on genomic coordinates
which <- RangesList(seq1=IRanges(1000, 2000),
                    seq2=IRanges(c(100, 1000), c(1000, 2000)))
p1 <- ScanBamParam(which=which)

## subset of reads based on 'flag' value
p2 <- ScanBamParam(flag=scanBamFlag(isMinusStrand=FALSE))

## subset of fields
p3 <- ScanBamParam(what=c("rname", "strand", "pos", "qwidth"))
                
## use
fl <- system.file("extdata", "ex1.bam", package="Rsamtools")
res <- scanBam(fl, param=p2)[[1]]
lapply(res, head)

## tags; NM: edit distance; H1: 1-difference hits
p4 <- ScanBamParam(tag=c("NM", "H1"), what="flag")
bam4 <- scanBam(fl, param=p4)
str(bam4[[1]][["tag"]])

## flag utils
flag <- scanBamFlag(isUnmappedQuery=FALSE, isMinusStrand=TRUE)
flag
bamFlagAsBitMatrix(flag)
flag4 <- bam4[[1]][["flag"]]
bamFlagAsBitMatrix(flag4[1:9])

[Package Rsamtools version 1.6.3 Index]