Skip to contents

Trimmed Mean of M-values (TMM) normalization of a phyloseq object

Source: R/normalize_pq.R
tmm_pq.Rd

lifecycle-experimental

Wrapper around edgeR::calcNormFactors() with method = "TMM" (Robinson & Oshlack 2010, doi:10.1186/gb-2010-11-3-r25 ). Returns counts-per-million scaled by the TMM-derived library sizes.

Usage

tmm_pq(physeq, log = FALSE)

Arguments

physeq

(required) a phyloseq-class object obtained using the phyloseq package.

log

(logical, default FALSE) if TRUE, returns log2(cpm + 1).

Value

A new phyloseq-class object with a TMM normalised otu_table.

See also

edgeR::calcNormFactors(), edgeR::cpm()

Author

Adrien Taudière

Examples

data_f_tmm <- tmm_pq(data_fungi_mini)
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf