mergeData: Map the annotation file to the count and tpm data

In RGLab/RNASeqPipelineR: Construct Standardized pipelines for processing RNASeq data

Description

Match the count, tpm, and feature data to the annotation file. Remove samples in count and tpm that are not found in the annotation file and ensure that the count and tpm columns match the rows of the annoation file. Also attach the results of the quality_control table to the annotation file.

Usage

mergeData(annotationMatch = NULL, mergeAnnotation = TRUE)

Arguments

annotationMatch	Column name of annotation file that maps to the column names of the count and tpm data sets (fastq file names with the suffixes removed including paired end identifiers if they exist). Default column name used is 'Sample'. Each row is a sample library and the columns are the annotation information
mergeAnnotation	If TRUE add annotation information contained in a .csv file in RAW_ANNOTATIONS directory.

Value

list list containing the count, tpm, feature, and annotation data. list names are counts, tpms, featureData, annoData.

The annotation file, which contains the experimental design information, must be constructed by the user and placed in the RAW_ANNOTATIONS directory. It must be a .csv file and be the only .csv file in the RAW_ANNOTATION directory. By default 'mergeData' will look for a column called 'Sample' that maps each row of the annotation file to the columns of the counts and tpm columns. The quality control matrix is generated by running 'runFASTQ' and then 'QualityControl'

RGLab/RNASeqPipelineR documentation built on Jan. 19, 2020, 12:31 a.m.