Description

Perform differential proportionality analysis

Input

name:type
description
pattern

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

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

name:type
description
pattern

results_genewise

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

genewise_plot

meta: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

*.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

rdata

meta:file

(Optional) R data containing propd object

*.propd.rds

*.propd.rds:file

(Optional) R data containing propd object

*.propd.rds

results_pairwise

meta: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

*.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

results_pairwise_filtered

meta:file

(Optional) TSV-format table of the filtered propd pairwise results. This table contains the pairs of genes with significant differential
proportionality values.

*.propd.pairwise_filtered.tsv

*.propd.pairwise_filtered.tsv:file

(Optional) TSV-format table of the filtered propd pairwise results. This table contains the pairs of genes with significant differential
proportionality values.

*.propd.pairwise_filtered.tsv

adjacency

meta: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

*.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

fdr

meta: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

*.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

session_info

*.R_sessionInfo.log:file

dump of R SessionInfo

*.R_sessionInfo.log

versions

versions.yml:file

File containing software versions

versions.yml