Nextflow Registry | nf-core/propr/propd@0.0.0-6c4ed3a

nf-core/propr/propd @ 0.0.0-6c4ed3a

Perform differential proportionality analysis

differential proportionality logratio expression propr propd

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @suzannejin @caraiz2001

Maintainers: @suzannejin

Perform differential proportionality analysis

Add the following snippet to your workflow script to include this module.

include { PROPR_PROPD } from 'nf-core/propr/propd'

MIT License

Process

`Name`	`PROPR_PROPD`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing contrast information. This can be used at the workflow level to pass optional parameters to the module, e.g. [ id:'contrast1', blocking:'patient' ] passed in as ext.args like: '--blocking_variable $meta.blocking'.
`contrast_variable` string	The column in the sample sheet that should be used to define groups for comparison
`reference` string	The value within the contrast_variable column of the sample sheet that should be used to derive the reference samples
`target` string	The value within the contrast_variable column of the sample sheet that should be used to derive the target samples

#2 tuple

`meta2` map	Groovy map containing study-wide metadata related to the sample sheet and matrix
`samplesheet` file	CSV or TSV format sample sheet with sample metadata
`counts` file	Raw TSV or CSV format expression matrix as output from the nf-core RNA-seq workflow

Output 9 channels

#1 fdr tuple

`meta` file	TSV-format table of genes associated with differential expression information as compiled from the propd results `*.propd.genewise.tsv`
`*.propd.fdr.tsv` file	(Optional) TSV-format table of FDR values. When permutation tests is performed, this table is generated with the FDR values calculated by the permutation tests. This is a more conservative test than the default BH method, but more computationally expensive. `*.propd.fdr.tsv`

#2 rdata tuple

`meta` file	TSV-format table of genes associated with differential expression information as compiled from the propd results `*.propd.genewise.tsv`
`*.propd.rds` file	(Optional) R data containing propd object `*.propd.rds`

#3 versions

`versions.yml` file	File containing software versions `versions.yml`

#4 adjacency tuple

`meta` file	TSV-format table of genes associated with differential expression information as compiled from the propd results `*.propd.genewise.tsv`
`*.propd.adjacency.csv` file	(Optional) CSV-format table of the adjacency matrix defining a graph, with edges (1) associated to pairs of genes that are significantly differentially proportional. `*.propd.adjacency.csv`

#5 session_info

`*.R_sessionInfo.log` file	dump of R SessionInfo `*.R_sessionInfo.log`

#6 genewise_plot tuple

`meta` file	TSV-format table of genes associated with differential expression information as compiled from the propd results `*.propd.genewise.tsv`
`*.propd.genewise.png` file	PNG-format plot of accumulated between group variance vs median log fold change. Genes with high between group variance and high log fold change are likely to be differentially expressed. `*.propd.genewise.png`

#7 results_genewise tuple

`meta` file	TSV-format table of genes associated with differential expression information as compiled from the propd results `*.propd.genewise.tsv`
`*.propd.genewise.tsv` file	TSV-format table of genes associated with differential expression information as compiled from the propd results `*.propd.genewise.tsv`

#8 results_pairwise tuple

`meta` file	TSV-format table of genes associated with differential expression information as compiled from the propd results `*.propd.genewise.tsv`
`*.propd.pairwise.tsv` file	(Optional) TSV-format table of the native propd pairwise results. This table contains the differential proportionality values associated to each pair of genes. `*.propd.pairwise.tsv`

#9 results_pairwise_filtered tuple

`meta` file	TSV-format table of genes associated with differential expression information as compiled from the propd results `*.propd.genewise.tsv`