find_ampliseq: Find and read-in AmpliSeq files
In ribiosIO: Input/Output Utilities of the 'ribios' Suite

find_ampliseq

R Documentation

Find and read-in AmpliSeq files

Description

Find and read-in AmpliSeq files into an expression matrix

Usage

find_ampliseq(dir)

read_ampliseq(files)

find_and_read_ampliseq(dir)

Arguments

`dir`	The top-level directory where a AmpliSeq run is saved. An example: ‘/data64/sequencing/iontorrent_data/Auto_user_PR1-139-AmpliSeqRNA_pathway_FD14_277_360/’
`files`	AmpliSeq files, potentially found by `find_ampliseq`

Details

Directory is recursively checked for files that match the name pattern ‘*.cov.xls’ (cov means coverage). Invalid links (judged by file size) are excluded.

Only data of total read counts are read-in.

Value

find_ampliseq returns a character vector of full names of valid files.

read_ampliseq returns a numeric matrix of gene expression in counts. Row names are unique gene names.

find_and_read_ampliseq combines the two functions and returns the expression matrix as read_ampliseq does.

Author(s)

Jitao David Zhang <jitao_david.zhang@roche.com>

Examples


ampdir <- system.file("extdata/ampliseq-data", package="ribiosIO")
ampfiles <- find_ampliseq(ampdir)
ampmat <- read_ampliseq(ampfiles)

ampmat.onestep <- find_and_read_ampliseq(ampdir)

ribiosIO documentation built on Feb. 20, 2026, 5:09 p.m.