importGInteractions {trackViewer} | R Documentation |
Read a track
object from a ginteractions, hic, mcool, or validPairs file
importGInteractions( file, format = c("ginteractions", "hic", "cool", "validPairs"), ranges = GRanges(), ignore.strand = TRUE, out = c("track", "GInteractions"), resolution = 1e+05, unit = c("BP", "FRAG"), normalization = c("NONE", "VC", "VC_SORT", "KR", "balanced"), ... )
file |
The path to the file to read. |
format |
The format of import file. Could be ginteractions, hic, cool or validPairs |
ranges |
An object of |
ignore.strand |
ignore the strand or not when do filter. default TRUE |
out |
output format. Default is track. Possible values: track, GInteractions. |
resolution |
Resolutions for the interaction data. |
unit |
BP (base pair) or FRAG (fragment) (.hic file only). |
normalization |
Type of normalization, NONE, VC, VC_SORT or KR for .hic and NONE, balanced for .cool. |
... |
NOT used. |
a track
object
See Also as importBam
, track
,
viewTracks
#import a ginteractions file #gi <- system.file("extdata", "test.ginteractions.tsv", package="trackViewer", # mustWork=TRUE) #dat <- importGInteractions(file=gi, format="ginteractions", # ranges=GRanges("chr7", IRanges(127471197, 127474697))) ##import a hic file hic <- system.file("extdata", "test_chr22.hic", package = "trackViewer", mustWork=TRUE) dat <- importGInteractions(file=hic, format="hic", ranges=GRanges("22", IRanges(1500000, 100000000))) ##import a cool file cool <- system.file("extdata", "test.mcool", package = "trackViewer", mustWork=TRUE) dat <- importGInteractions(file=cool, format="cool", resolution = 2, ranges=GRanges("chr1", IRanges(10, 28))) ##import a validPairs file #validPairs <- system.file("extdata", "test.validPairs", package = "trackViewer", # mustWork=TRUE) #dat <- importGInteractions(file=validPairs, format="validPairs")