read in bam files

wraper for readGAlignments/readGAlignmentsList to read in bam files.

readBamFile(
  bamFile,
  which,
  tag = character(0),
  what = c("qname", "flag", "mapq", "isize", "seq", "qual", "mrnm"),
  flag = scanBamFlag(isSecondaryAlignment = FALSE, isUnmappedQuery = FALSE,
    isNotPassingQualityControls = FALSE, isSupplementaryAlignment = FALSE),
  asMates = FALSE,
  bigFile = FALSE,
  ...
)

Arguments

bamFile	character(1). Bam file name.
which	A GRanges, IntegerRangesList, or any object that can be coerced to a RangesList, or missing object, from which a IRangesList instance will be constructed. See ScanBamParam.
tag	A vector of characters indicates the tag names to be read. See ScanBamParam.
what	A character vector naming the fields to return. Fields are described on the Rsamtools[scanBam] help page.
flag	An integer(2) vector used to filter reads based on their 'flag' entry.
asMates	logical(1). Paired ends or not
bigFile	If the file take too much memory, set it to true to avoid read the reads into memory. scanBamFlag helper function.
...	parameters used by readGAlignmentsList or readGAlignments

Value

A GAlignmentsList object when asMates=TRUE, otherwise A GAlignments object. If bigFile is set to TRUE, no reads will be read into memory at this step and empty GAlignments/GAlignmentsList will be returned.

Author

Jianhong Ou

Examples

library(BSgenome.Hsapiens.UCSC.hg19)
which <- as(seqinfo(Hsapiens)["chr1"], "GRanges")
bamfile <- system.file("extdata", "GL1.bam", 
                       package="ATACseqQC", mustWork=TRUE)
readBamFile(bamfile, which=which, asMates=TRUE)
#> GAlignmentsList object of length 44357:
#> [[1]]
#> GAlignments object with 2 alignments and 7 metadata columns:
#>       seqnames strand       cigar    qwidth     start       end     width
#>          <Rle>  <Rle> <character> <integer> <integer> <integer> <integer>
#>   [1]     chr1      +         47M        47    567414    567460        47
#>   [2]     chr1      -         50M        50    567544    567593        50
#>           njunc |       qname      flag      mapq     isize
#>       <integer> | <character> <integer> <integer> <integer>
#>   [1]         0 |         100        99        30       180
#>   [2]         0 |         100       147        30      -180
#>                           seq                    qual     mrnm
#>                <DNAStringSet>          <PhredQuality> <factor>
#>   [1] ATTTAGCTGA...AAATGATCTG CCCFFFFFHH...JJJJJJJJJJ     chr1
#>   [2] GACATCGTAC...TCCACTATGT JJJJJJJHHJ...HHFFFFFCCC     chr1
#>   -------
#>   seqinfo: 25 sequences from an unspecified genome
#> 
#> [[2]]
#> GAlignments object with 2 alignments and 7 metadata columns:
#>       seqnames strand       cigar    qwidth     start       end     width
#>          <Rle>  <Rle> <character> <integer> <integer> <integer> <integer>
#>   [1]     chr1      -         50M        50 101701613 101701662        50
#>   [2]     chr1      +         50M        50 101701398 101701447        50
#>           njunc |       qname      flag      mapq     isize
#>       <integer> | <character> <integer> <integer> <integer>
#>   [1]         0 |      100003        83        42      -265
#>   [2]         0 |      100003       163        42       265
#>                           seq                    qual     mrnm
#>                <DNAStringSet>          <PhredQuality> <factor>
#>   [1] TGAATCTCTC...ACCTCTCCAT FFFFFFGHHH...FHFDEDFCB@     chr1
#>   [2] GACCAAGTCC...CTAAGCAAAA @CCFFFFEHG...JJIGJIJJIJ     chr1
#>   -------
#>   seqinfo: 25 sequences from an unspecified genome
#> 
#> [[3]]
#> GAlignments object with 2 alignments and 7 metadata columns:
#>       seqnames strand       cigar    qwidth     start       end     width
#>          <Rle>  <Rle> <character> <integer> <integer> <integer> <integer>
#>   [1]     chr1      +         50M        50 101701631 101701680        50
#>   [2]     chr1      -         50M        50 101701766 101701815        50
#>           njunc |       qname      flag      mapq     isize
#>       <integer> | <character> <integer> <integer> <integer>
#>   [1]         0 |      100005        99        42       185
#>   [2]         0 |      100005       147        42      -185
#>                           seq                    qual     mrnm
#>                <DNAStringSet>          <PhredQuality> <factor>
#>   [1] GCAGCAGCCC...ATCTGGGACA CC@FFFFFHH...JIJJIJJIJE     chr1
#>   [2] AAAGCCACTG...GGATCTGGGG DHHIIIIJIH...HHFFFFFCCC     chr1
#>   -------
#>   seqinfo: 25 sequences from an unspecified genome
#> 
#> ...
#> <44354 more elements>