readTargets: Creates sample list and BAM/BED file list from file

In pmoulos/metaseqR2: An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms

Creates sample list and BAM/BED file list from file

Description

Create the main sample list and determine the BAM/BED files for each sample from an external file.

Usage

    readTargets(input, path = NULL)

Arguments

input	a tab-delimited file or a YAML file specifically structured. See Details.
path	an optional path where all the BED/BAM files are placed, to be prepended to the BAM/BED file names in the targets file.

Details

Regarding the input file, this can be a simple text tab-delimited file or a YAML file describing the data to be analyzed.

Regarding the tab-delimited version, its columns must be structured as follows: the first line of the external tab delimited file should contain column names (names are not important). The first column MUST contain UNIQUE sample names. The second column MUST contain the raw BAM/BED files WITH their full path. Alternatively, the path argument should be provided (see below). The third column MUST contain the biological condition where each of the samples in the first column should belong to. There is an optional fourth column which should contain the keywords "single" for single-end reads, "paired" for paired-end reads or "mixed" for BAM files that contain both single- and paired-end reads (e.g. after a mapping procedure with two round of alignment). If this column is not provided, single-end reads will be assumed. There is an optional fifth column which stranded read assignment. It should contain the keywords "forward" for a forward (5'->3') strand library construction protocol, "reverse" for a reverse (3'->5') strand library construction protocol, or "no" for unstranded/unknown protocol. If this column is not provided, unstranded reads will be assumed.

Regarding the YAML version, the same instructions apply, but this time instead of columns, the data are provided as a YAML array under a keyword/top-level field representing the respective header in the tab-delimited version. Alternatively, the aforementioned structure can be nested under a root level named strictly either targets or metaseqR2_targets. The latter can be especially useful when incorporating the metaseqR2 pipeline in a wider pipeline including various analyses and described using a workflow language such as CWL.

Value

A named list with four members. The first member is a named list whose names are the conditions of the experiments and its members are the samples belonging to each condition. The second member is like the first, but this time the members are named vectors whose names are the sample names and the vector elements are full path to BAM/BED files. The third member is like the second, but instead of filenames it contains information about single- or paired-end reads (if available). The fourth member is like the second, but instead of filenames it contains information about the strandedness of the reads (if available). The fifth member is the guessed type of the input files (SAM/BAM or BED). It will be used if not given in the main read2count function.

Author(s)

Panagiotis Moulos

Examples

dataPath <- system.file("extdata",package="metaseqR2")
targets <- data.frame(samplename=c("C","T"),
    filename=file.path(dataPath,c("C.bam","T.bam")),  
    condition=c("Control","Treatment"),
    paired=c("single","single"),stranded=c("forward","forward"))
path <- tempdir()

# Tab delimited case
write.table(targets,file=file.path(path,"targets.txt"),
    sep="\t",row.names=FALSE,quote=FALSE)
theList <- readTargets(file.path(path,"targets.txt"),path=path)
sampleList <- theList$samples
bamfileList <- theList$files

# YAML case
require(yaml)
write_yaml(as.list(targets),file.path(path,"targets.yml"))
theYList <- readTargets(file.path(path,"targets.yml"),path=path)
identical(theList,theYList) # TRUE

# YAML case with nested targets
write_yaml(list(targets=as.list(targets)),
    file.path(path,"targets2.yml"))
theYList2 <- readTargets(file.path(path,"targets2.yml"),path=path)
identical(theYList,theYList2) # TRUE

pmoulos/metaseqR2 documentation built on May 20, 2024, 5:48 a.m.