importGInteractions: Reading data from a ginteractions, hic, cool, or validPairs...

In jianhong/trackViewer: A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data

Reading data from a ginteractions, hic, cool, or validPairs file

Description

Read a track object from a ginteractions, hic, mcool, or validPairs file

Usage

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", "SCALE", "GW_KR", "GW_SCALE", "GW_VC",
    "INTER_KR", "INTER_SCALE", "INTER_VC", "balanced"),
  matrixType = c("observed", "oe", "expected"),
  ...
)

Arguments

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 GRanges to indicate the range to be imported. For .hic file, if the length of ranges is 2, the first range will be used as anchor 1 and the second range will be used as anchor 2.
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.
matrixType	Type of matrix for .hic file. Available choices are "observed", "oe", and "expected". default is "observed".
...	NOT used.

Value

a track object

See Also

See Also as listResolutions, listChromosomes, readHicNormTypes

Examples

#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
if(.Platform$OS.type!="windows"){
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")

jianhong/trackViewer documentation built on March 17, 2024, 2:16 p.m.