modules/propr_propr

Perform logratio-based correlation analysis -> get proportionality & basis shrinkage partial correlation coefficients. One can also compute standard correlation coefficients, if required.

coexpressioncorrelationproportionalitylogratioproprcorpcor

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

Description

Perform logratio-based correlation analysis -> get proportionality & basis shrinkage partial correlation coefficients. One can also compute standard correlation coefficients, if required.

Input

name:type

description

pattern

`meta:map`

Groovy Map containing sample information. This can be used at the workflow level to pass optional parameters to the module. [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 replaced by the minimun number. It is recommended to handle the zeros beforehand with the method of preference.

*.{csv,tsv}

Output

name:type

description

pattern

`propr`

`meta:map`

Groovy Map containing sample information. This can be used at the workflow level to pass optional parameters to the module. [id: ‘test’, …]

`*.propr.rds:file`

R propr object

*.propr.rds

`matrix`

`meta:map`

Groovy Map containing sample information. This can be used at the workflow level to pass optional parameters to the module. [id: ‘test’, …]

`*.propr.tsv:file`

Coefficient matrix

*.propr.tsv

`fdr`

`meta:map`

Groovy Map containing sample information. This can be used at the workflow level to pass optional parameters to the module. [id: ‘test’, …]

`*.fdr.tsv:file`

(optional) propr fdr table

*.fdr.tsv

`adj`

`meta:map`

Groovy Map containing sample information. This can be used at the workflow level to pass optional parameters to the module. [id: ‘test’, …]

`*.adj.csv:file`

(optional) propr adjacency table

*.adj.csv

`warnings`

`*.warnings.log:file`

Warnings

*.warnings.log

`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

corpcor
GPL >=3

Efficient Estimation of Covariance and (Partial) Correlation

cran.r-project.org/web/packages/corpcor cran.r-project.org/web/packages/corpcor/corpcor.pdf 10.2202/1544-6115.1175

modules/propr_propr

Description

Input

`meta:map`

`count:file`

Output

`propr`

`meta:map`

`*.propr.rds:file`

`matrix`

`meta:map`

`*.propr.tsv:file`

`fdr`

`meta:map`

`*.fdr.tsv:file`

`adj`

`meta:map`

`*.adj.csv:file`

`warnings`

`*.warnings.log:file`

`session_info`

`*.R_sessionInfo.log:file`

`versions`

`versions.yml:file`

Tools

propr
GPL-2

corpcor
GPL >=3

maintainer

get in touch

modules/propr_propr

Description

Input

meta:map

count:file

Output

propr

meta:map

*.propr.rds:file

matrix

meta:map

*.propr.tsv:file

fdr

meta:map

*.fdr.tsv:file

adj

meta:map

*.adj.csv:file

warnings

*.warnings.log:file

session_info

*.R_sessionInfo.log:file

versions

versions.yml:file

Tools

propr GPL-2

corpcor GPL >=3

maintainer

get in touch

`meta:map`

`count:file`

`propr`

`meta:map`

`*.propr.rds:file`

`matrix`

`meta:map`

`*.propr.tsv:file`

`fdr`

`meta:map`

`*.fdr.tsv:file`

`adj`

`meta:map`

`*.adj.csv:file`

`warnings`

`*.warnings.log:file`

`session_info`

`*.R_sessionInfo.log:file`

`versions`

`versions.yml:file`

propr
GPL-2

corpcor
GPL >=3