read.lefse.Rd
This reads an input file in a LEfSe input format
read.lefse(filename = "data.txt", rows.meta = 1, row.samples = 2)
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 |
a list with two elements:
feat
a features matrix
meta
a metadate matrix
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")#>#> #> #>#>#>#>#>#>#>#>