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:

- `feat` a features matrix

- `meta` a metadate matrix

### 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 1.2.1 Index]