importData: Import Array Data

In anschue/toxprofileR: Functions for Retrieving Dynamic Toxicogenomic Fingerprints

Description

This function builds on the limma function read.maimages and imports raw data from a time and concentration dependent toxicogenomic experiment. It removes outlier arrays based on the KS.test, and outlier test based on sum and 75 returns an EListRaw.

Usage

importData(targetfile, datadir, scanID = 1, output = T,
  removeOutliers = T, qc_coeff = c(ks = 3, sum = 3, iqr = 3, q = 3, d =
  1), qc_sum = 1)

Arguments

targetfile	string, name of targetfile .csv, should contain columns named FileName, sample_ID, substance, concentration_level, concentration_umol_l, time_hpe, type, comment, and scan_ID
datadir	string, path to raw data
scanID	numerical, ID of scan (default: 1)
output	logical, should function return target (default: T)
removeOutliers	logical, should outliers be removed
qc_coeff	A named character vector giving the coefficient for acceptable intervals
qc_sum	Number of tests leading to array exclusion

Value

EListraw (limma class)

anschue/toxprofileR documentation built on Nov. 2, 2019, 1:55 p.m.