modules/propr_logratio

Transform the data matrix using centered logratio transformation (CLR) or additive logratio transformation (ALR)

alrclrlogratioboxcoxtransformationpropr

https://github.com/nf-core/modules/[...]/modules/nf-core/propr/logratio

Description

Transform the data matrix using centered logratio transformation (CLR) or additive logratio transformation (ALR)

Input

name:type

description

pattern

`meta:map`

Groovy Map containing additional information. meta.id can be used to name the output files. [id: ‘test’, …]

`count:file`

Count matrix, where rows = variables or genes, columns = samples or cells. This matrix should not contain zeros. Otherwise, they will be first replaced by the minimum value. You may want to handle the zeros with a different method beforehand.

*.{csv,tsv}

Output

name:type

description

pattern

`logratio`

`meta:map`

Groovy Map containing additional information. meta.id can be used to name the output files. [id: ‘test’, …]

`*.logratio.tsv:file`

ALR/CLR transformed data matrix. With rows = variables or genes, columns = samples or cells.

*.logratio.tsv

`session_info`

`*.R_sessionInfo.log:file`

dump of R SessionInfo

*.R_sessionInfo.log

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

propr
GPL-2

Logratio methods for omics data

github.com/tpq/propr rdrr.io/cran/propr/man/propr https://github.com/tpq/propr 10.1038/s41598-017-16520-0

modules/propr_logratio

Description

Input

meta:map

count:file

Output

logratio

meta:map

*.logratio.tsv:file

session_info

*.R_sessionInfo.log:file

versions

versions.yml:file

Tools

propr GPL-2

`meta:map`

`count:file`

`logratio`

`meta:map`

`*.logratio.tsv:file`

`session_info`

`*.R_sessionInfo.log:file`

`versions`

`versions.yml:file`

propr
GPL-2