getData: Get coordinated data from a compressed file for RIVER

In RIVER: R package for RIVER (RNA-Informed Variant Effect on Regulation)

Description

getData extracts genomic features, z-scores of gene expression, and N2 pairs having same rare variants from an imported compressed data, computes outlier status from z-scores given a z-score threshold and coordinates the genomic features, outlier status, and a list of N2 pairs into ExpressionSet class having standardized data structure.

Usage

getData(filename = system.file("extdata", "simulation_RIVER.gz", package =
  "RIVER"), ZscoreThrd = 1.5)

Arguments

filename	A full path of a compressed input file that consists of all samples in rows and subject ID, gene name, genomic features, z-scores of corresponding gene expression, and a list of N2 pairs in columns from left to right. In N2 pairs, samples not paired with othersamples have NA while two samples sharing same rare variant near a gene have same pre-assigend integers.
ZscoreThrd	A |Z-score| threshold for defining outlier status of samples

Value

dataInput An object of ExpressionSet class which contains input data required for all functions in RIVER including genomic features, outlier status, and N2 pairs.

Author(s)

Yungil Kim, [e-mail]

See Also

fread, ExpressionSet,

Examples

InputData <- getData(filename=system.file("extdata", "simulation_RIVER.gz",
        package = "RIVER"), ZscoreThrd=1.5)

RIVER documentation built on Nov. 8, 2020, 6:54 p.m.