This function takes bam file paths and read them into GRanges objects. Note: Can be quite lengthy for .bam files with 5+ millions fragments.
importPEBamFiles(
files,
genome = NULL,
where = NULL,
max_insert_size = 1000,
shift_ATAC_fragments = FALSE,
cores = 10,
verbose = TRUE
)character vector, each element of the vector is the path of an individual .bam file.
character, genome ID (e.g. "sacCer3", "ce11", "dm6", "mm10" or "hg38").
GRanges, only import the fragments mapping to the input GRanges (can fasten the import process a lot).
Integer, filter out fragments larger than this size.
Boolean, if the fragments come from ATAC-seq, one might want to shift the extremities by +5 / -4 bp.
Integer, number of cores to use when indexing bam files
Boolean
A GRanges object containing fragments from the input .bam file.
bamfile <- system.file("extdata", "ex1.bam", package = "Rsamtools")
fragments <- importPEBamFiles(
bamfile,
shift_ATAC_fragments = TRUE
)
#> > Importing /__w/_temp/Library/Rsamtools/extdata/ex1.bam ...
#> > Filtering /__w/_temp/Library/Rsamtools/extdata/ex1.bam ...
#> > Shifting /__w/_temp/Library/Rsamtools/extdata/ex1.bam ...
#> > /__w/_temp/Library/Rsamtools/extdata/ex1.bam import completed.
fragments
#> GRanges object with 1572 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> [1] seq1 41-215 +
#> [2] seq1 54-255 +
#> [3] seq1 56-258 +
#> [4] seq1 65-255 +
#> [5] seq1 65-265 +
#> ... ... ... ...
#> [1568] seq2 1326-1542 -
#> [1569] seq2 1336-1544 -
#> [1570] seq2 1358-1550 -
#> [1571] seq2 1380-1557 -
#> [1572] seq2 1353-1562 -
#> -------
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths