quickBamFlagSummary: Group the records of a BAM file based on their flag bits and...
In Rsamtools: Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

Description Usage Arguments Value Author(s) References See Also Examples

quickBamFlagSummary groups the records of a BAM file based on their flag bits and counts the number of records in each group.

quickBamFlagSummary(file, ..., param=ScanBamParam(), main.groups.only=FALSE)

## S4 method for signature 'character'
quickBamFlagSummary(file, index=file, ..., param=ScanBamParam(),
    main.groups.only=FALSE)

## S4 method for signature 'list'
quickBamFlagSummary(file, ..., param=ScanBamParam(), main.groups.only=FALSE)

`file, index`	For the character method, the path to the BAM file to read, and to the index file of the BAM file to read, respectively. For the list() method, `file` is a named list with elements “qname” and “flag” with content as from `scanBam`.
`...`	Additional arguments, perhaps used by methods.
`param`	An instance of `ScanBamParam`. This determines which records are considered in the counting.
`main.groups.only`	If `TRUE`, then the counting is performed for the main groups only.

Nothing is returned. A summary of the counts is printed to the console unless redirected by sink.

Hervé Pagès

http://samtools.sourceforge.net/

scanBam, ScanBamParam.

BamFile for a method for that class.

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bamfile <- system.file("extdata", "ex1.bam", package="Rsamtools",
                       mustWork=TRUE)
quickBamFlagSummary(bamfile)

Loading required package: GenomeInfoDb
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

                                group |    nb of |    nb of | mean / max
                                   of |  records |   unique | records per
                              records | in group |   QNAMEs | unique QNAME
All records........................ A |     3307 |     1699 | 1.95 / 2
  o template has single segment.... S |        0 |        0 |   NA / NA
  o template has multiple segments. M |     3307 |     1699 | 1.95 / 2
      - first segment.............. F |     1654 |     1654 |    1 / 1
      - last segment............... L |     1653 |     1653 |    1 / 1
      - other segment.............. O |        0 |        0 |   NA / NA

Note that (S, M) is a partitioning of A, and (F, L, O) is a partitioning of M.
Indentation reflects this.

Details for group M:
  o record is mapped.............. M1 |     3271 |     1699 | 1.93 / 2
      - primary alignment......... M2 |     3271 |     1699 | 1.93 / 2
      - secondary alignment....... M3 |        0 |        0 |   NA / NA
  o record is unmapped............ M4 |       36 |       36 |    1 / 1

Details for group F:
  o record is mapped.............. F1 |     1641 |     1641 |    1 / 1
      - primary alignment......... F2 |     1641 |     1641 |    1 / 1
      - secondary alignment....... F3 |        0 |        0 |   NA / NA
  o record is unmapped............ F4 |       13 |       13 |    1 / 1

Details for group L:
  o record is mapped.............. L1 |     1630 |     1630 |    1 / 1
      - primary alignment......... L2 |     1630 |     1630 |    1 / 1
      - secondary alignment....... L3 |        0 |        0 |   NA / NA
  o record is unmapped............ L4 |       23 |       23 |    1 / 1