read.lefse {SIAMCAT}R Documentation

read an input file in a LEfSe input format

Description

This reads an input file in a LEfSe input format

Usage

read.lefse(filename = "data.txt", rows.meta = 1, row.samples = 2)

Arguments

filename

name of the input file in a LEfSe input format

rows.meta

specifies in which rows medata variables are stored

row.samples

specifies in which row sample names are stored

Value

a list with two elements:

Examples


fn.in.lefse<- system.file("extdata",
"LEfSe_crc_zeller_msb_mocat_specI.tsv",package = "SIAMCAT")
meta.and.features <- read.lefse(fn.in.lefse, rows.meta = 1:6,
row.samples = 7)
meta <- meta.and.features$meta
feat <- meta.and.features$feat
label <- create.label(meta=meta, label="label", case = "cancer")
siamcat <- siamcat(feat=feat, label=label, meta=meta)


[Package SIAMCAT version 1.13.4 Index]