hiReadsProcessor (version 1.8.2)

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

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, interactive = TRUE)

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 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.

interactive

whether to prompt each time the function encounters an issue or use the defaults. Default is TRUE.

Value

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

See Also

read.sampleInfo, findBarcodes, splitByBarcode

Examples

runData <- system.file("extdata/FLX_sample_run/",
package = "hiReadsProcessor")
read.SeqFolder(runData, seqfilePattern=".+fna.gz$")
read.SeqFolder(".", seqfilePattern="\\.TCA.454Reads.fna$")
read.SeqFolder(".", seqfilePattern=".+fastq$")
read.SeqFolder(".", seqfilePattern=".+sff$")