readTargets {metaseqR2} | R Documentation |
Create the main sample list and determine the BAM/BED files for each sample from an external file.
readTargets(input, path = NULL)
input |
a tab-delimited 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. |
Regarding the input file, its files 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.
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.
Panagiotis Moulos
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() 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