This is a lightweight wrapper to the import family of functions defined in rtracklayer.
Read common interval based formats as GRanges.
read_bed(file, col_names = NULL, genome_info = NULL, overlap_ranges = NULL)
read_bed_graph(
file,
col_names = NULL,
genome_info = NULL,
overlap_ranges = NULL
)
read_narrowpeaks(
file,
col_names = NULL,
genome_info = NULL,
overlap_ranges = NULL
)A path to a file or a connection.
An optional character vector for including additional
columns in file that are not part of the BED/narrowPeaks specification.
An optional character string or a Ranges object that contains information about the genome build. For example the USSC identifier "hg19" will add build information to the returned GRanges.
An optional Ranges object. Only the intervals in the file that overlap the Ranges will be returned.
A GRanges object
This is a lightweight wrapper to the import family
of functions defined in rtracklayer.
The read_narrowpeaks function parses the ENCODE narrowPeak BED format (see
https://genome.ucsc.edu/FAQ/FAQformat.html#format12 for details.). As
such the parser expects four additional columns called (corresponding to
the narrowPeaks spec):
signalValue
pValue
qValue
peak
rtracklayer::BEDFile()
test_path <- system.file("tests", package = "rtracklayer")
bed_file <- file.path(test_path, "test.bed")
gr <- read_bed(bed_file)
gr
#> GRanges object with 5 ranges and 5 metadata columns:
#> seqnames ranges strand | name score itemRgb
#> <Rle> <IRanges> <Rle> | <character> <numeric> <character>
#> [1] chr7 127471197-127472363 + | Pos1 0 #FF0000
#> [2] chr7 127472364-127473530 + | Pos2 2 #FF0000
#> [3] chr7 127473531-127474697 - | Neg1 0 #FF0000
#> [4] chr9 127474698-127475864 + | Pos3 5 #FF0000
#> [5] chr9 127475865-127477031 - | Neg2 5 #0000FF
#> thick blocks
#> <IRanges> <IRangesList>
#> [1] 127471197-127472363 1-300,501-700,1068-1167
#> [2] 127472364-127473530 1-250,668-1167
#> [3] 127473531-127474697 1-1167
#> [4] 127474698-127475864 1-1167
#> [5] 127475865-127477031 1-1167
#> -------
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
gr <- read_bed(bed_file, genome_info = "hg19")
#>
#> Attaching package: ‘Biostrings’
#> The following object is masked from ‘package:base’:
#>
#> strsplit
#>
#> Attaching package: ‘rtracklayer’
#> The following object is masked from ‘package:BiocIO’:
#>
#> FileForFormat
gr
#> GRanges object with 5 ranges and 5 metadata columns:
#> seqnames ranges strand | name score itemRgb
#> <Rle> <IRanges> <Rle> | <character> <numeric> <character>
#> [1] chr7 127471197-127472363 + | Pos1 0 #FF0000
#> [2] chr7 127472364-127473530 + | Pos2 2 #FF0000
#> [3] chr7 127473531-127474697 - | Neg1 0 #FF0000
#> [4] chr9 127474698-127475864 + | Pos3 5 #FF0000
#> [5] chr9 127475865-127477031 - | Neg2 5 #0000FF
#> thick blocks
#> <IRanges> <IRangesList>
#> [1] 127471197-127472363 1-300,501-700,1068-1167
#> [2] 127472364-127473530 1-250,668-1167
#> [3] 127473531-127474697 1-1167
#> [4] 127474698-127475864 1-1167
#> [5] 127475865-127477031 1-1167
#> -------
#> seqinfo: 298 sequences (2 circular) from hg19 genome
olap <- as_granges(data.frame(seqnames = "chr7", start = 1, end = 127473000))
gr <- read_bed(bed_file,
overlap_ranges = olap)
# bedGraph
bg_file <- file.path(test_path, "test.bedGraph")
gr <- read_bed_graph(bg_file)
gr
#> GRanges object with 9 ranges and 1 metadata column:
#> seqnames ranges strand | score
#> <Rle> <IRanges> <Rle> | <numeric>
#> [1] chr19 59102001-59102300 * | -1.00
#> [2] chr19 59102301-59102600 * | -0.75
#> [3] chr19 59102601-59102900 * | -0.50
#> [4] chr19 59102901-59103200 * | -0.25
#> [5] chr19 59103201-59103500 * | 0.00
#> [6] chr19 59103501-59103800 * | 0.25
#> [7] chr17 59103801-59104100 * | 0.50
#> [8] chr18 59104101-59104400 * | 0.75
#> [9] chr18 59104401-59104700 * | 1.00
#> -------
#> seqinfo: 3 sequences from an unspecified genome; no seqlengths
# narrowpeaks
np_file <- system.file("extdata", "demo.narrowPeak.gz", package="rtracklayer")
gr <- read_narrowpeaks(np_file, genome_info = "hg19")
gr
#> GRanges object with 6 ranges and 6 metadata columns:
#> seqnames ranges strand | name score signalValue
#> <Rle> <IRanges> <Rle> | <character> <numeric> <numeric>
#> [1] chr19 893203-893659 * | <NA> 0 16.705
#> [2] chr19 45981393-45982404 * | <NA> 0 7.853
#> [3] chr9 137029517-137029957 * | <NA> 0 19.135
#> [4] chr7 148680558-148681129 * | <NA> 0 10.418
#> [5] chr7 148638202-148638769 * | <NA> 0 8.161
#> [6] chr6 52860024-52860589 * | <NA> 0 9.332
#> pValue qValue peak
#> <numeric> <numeric> <integer>
#> [1] 85.879 3.31125e-82 240
#> [2] 83.114 1.44562e-79 587
#> [3] 78.886 1.95499e-75 208
#> [4] 70.532 3.68097e-67 263
#> [5] 60.506 2.60538e-57 341
#> [6] 54.023 7.13040e-51 349
#> -------
#> seqinfo: 298 sequences (2 circular) from hg19 genome