MergeIndividualFiles: Merge Data from Multiple Files

In okg3/MultiDataAnalysis: Combine Data from Multiple Files or Experiments into One Analysis

Description

MergeIndividualFiles merges data from individual sample data and returns list of matrices.

Usage

MergeIndividualFiles(
  fileDirectory,
  filePattern = NULL,
  filePrefix = NULL,
  indVars = "auto",
  IDcol = 1,
  ...
)

Arguments

fileDirectory	a character vector of full path names to directory containing individual files.
filePattern	an optional regular expression. Only file names which match the regular expression will be returned. Strings matching regular expression will be removed from column names in returned dataset.
filePrefix	an optional regular expression. Strings matching regular expression will be removed from column names in returned dataset.
indVars	character vector of column names in individual files that correspond with individual measures (e.g. not annotation). Default value is all columns except those in IDcol.
IDcol	character or numeric vector of columns in individual files on which to merge
...	additional parameters to be passed to data.table::fread()

Details

This function reads in files containing data from individual samples and merges individual data into one dataset by variable or measurement.

Value

A list of merged data. The first list element contains annotations (e.g. columns that are not included in indVars). All other list elements are matrices with rownames matching values in IDcol and columns matching file names.

Examples

## Not run: 
out <- MergeIndividualFiles(
fileDirectory = paste0(path.package("MultiDataAnalysis"), "/extdata/"),
filePattern = ".txt.gz", indVars = c("AllSubs", "Coverage-q25", "MeanQ",
"BaseCount[A,C,G,T]", "Frequency", "Pvalue"),
IDcol = c("Region", "Position", "Reference", "Strand"))

## End(Not run)

okg3/MultiDataAnalysis documentation built on March 28, 2020, 12:20 p.m.