getSampleFromBucket: Import HiC Sample from AWS Bucket

In aryeelab/sparseHiC: Efficient compression and analysis of Hi-C Data

Description

getSampleFromBucket returns a sparseHiCdatum object when the user specifies the sample name and the bucket that the object is housed in. If the sample is split by chromosomes (e.g. GM12878 in the DNAlandscapeR bucket), then the function collates those into one object. However, the user can specify only certain chromosomes be imported using the chr paramter. As a side note, all AWS buckets are lower case letters only, so that may be a source of error when trying to import the bucket.

Usage

getSampleFromBucket(sample, bucket, chr = NA, organism = "human")

## S4 method for signature 'ANY'
getSampleFromBucket(sample, bucket, chr = NA,
  organism = "human")

Arguments

sample	The name of the sample (e.g. GM12878 or BT142-rep1)
bucket	Name of the AWS bucket.
chr	= NA Specify which chromosomes to pull down; if left with NA, then by default, all chromosomes will be pulled down
organism	= "human" or "mouse" likely supported

Value

A sparseHiCdatum object

Examples

# Import chromosome 4 from DNAlandscapeR bucket
samp <- "IMR90"
# hesc <- getSampleFromBucket(samp, "dnalandscaper", c("chr1", "chr4"))

aryeelab/sparseHiC documentation built on May 12, 2019, 3:43 a.m.