read.SeqFolder: Read contents of a sequencing folder and make a SimpleList...

In malnirav/hiReadsProcessor: Functions to process LM-PCR reads from 454/Illumina data

Description

Given a sequencing folder path, sample information file path, and sequence file extension pattern, the function returns a list of variables required to process the data. The function also calls read.sampleInfo which reads in sample processing metadata and formats it if needed.

Usage

read.SeqFolder(
  sequencingFolderPath = NULL,
  sampleInfoFilePath = NULL,
  seqfilePattern = NULL
)

Arguments

sequencingFolderPath	full or relative path to the sequencing folder
sampleInfoFilePath	full or relative path to the sample information file, which holds samples to quadrant/lane associations along with other metadata required to trim sequences or process it. Default to NULL, where the function tries to find xls/xlsx or tab deliminated txt file in the sequencing folder which sounds similar to 'sampleinfo' and present you with choices of file to select from.
seqfilePattern	regex/string to describe sequence file endings. See examples. Default is NULL.

Value

a SimpleList list which is used by other functions to process and decode the data.

Note

• One must make sure that each sequencing file has sector name/number prefixed at the beginning, else findBarcodes will fail trying to find the filename.

• For paired end Illumina runs, make sure the filenames include R1, R2, and I1 somewhere in the name denoting pair1, pair2, and index/barcode reads, respectively.

See Also

read.sampleInfo, findBarcodes, splitByBarcode

Examples

runData <- system.file("extdata/FLX_sample_run/", 
package = "hiReadsProcessor")
read.SeqFolder(runData, seqfilePattern=".+fna.gz$")
## Not run: 
read.SeqFolder(".", seqfilePattern = "\\.TCA.454Reads.fna$")
read.SeqFolder(".", seqfilePattern = ".+fastq$")

## End(Not run)

malnirav/hiReadsProcessor documentation built on July 29, 2021, 6:33 a.m.