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

Description Usage Arguments Value Note See Also Examples

View source: R/hiReadsProcessor.R

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

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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

See Also

read.sampleInfo, findBarcodes, splitByBarcode

Examples

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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)

hiReadsProcessor documentation built on Nov. 8, 2020, 5:43 p.m.