buildFileTable: buildFileTable

In DupChecker: a package for checking high-throughput genomic data redundancy in meta-analysis

Description

The function build file table in the subdirectories under root directories user provided. The result table contains two columns, dataset and filename

Usage

buildFileTable(rootDir, subDirPattern = NULL, filePattern = NULL,
  ignoreExtensions = c("tar", "md5"), ignore.case = TRUE)

Arguments

rootDir	the root of directories whose sub directories contains file waiting for validation. It can be vector of directories, or just one directory
subDirPattern	the pattern of sub directory name. Default is NULL.
filePattern	the pattern of file waiting for validation. For example, "cel$" for AffyMetrix CEL file only. Default is NULL.
ignoreExtensions	the extensions of file that will be ignored. Default is c("tar", "md5").
ignore.case	ignore the case difference when list files from sub directory using filePattern

Value

a data frame containing full file name and its corresponding dataset, which will be used at validateFile

Examples

rootDir<-paste0(dirname(tempdir()), "/DupChecker")
datafile<-buildFileTable(rootDir=rootDir, filePattern="cel$")
#or
datafile<-buildFileTable(rootDir=c(paste0(rootDir,
                         c("/E-MEXP-3872", "/GSE1478") )), filePattern="cel$")

DupChecker documentation built on April 28, 2020, 6:46 p.m.