Description

reads a maxQuant proteinGroups file with Proteus

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing contrast information, e.g. [ variable:‘treatment’, reference:‘treated’, control:‘saline’, blocking:” ]

samplesheet (file)

CSV or TSV format sample sheet with sample metadata; check here for specifications: https://rdrr.io/github/bartongroup/Proteus/man/readProteinGroups.html

intensities (file)

proteinGroups TXT file with protein intensities information from maxQuant; check here for specifications: https://rdrr.io/github/bartongroup/Proteus/man/readProteinGroups.html

meta2 (map)

Groovy Map containing contrast information, e.g. [ variable:‘treatment’, reference:‘treated’, control:‘saline’, blocking:” ]

contrast_variable (string)

The column in the sample sheet that should be used to define groups for comparison

Output

Name (Type)
Description
Pattern

dendro_plot (file)

PNG file; dendrogram of the normalized samples hierarchically clustered by their intensities

mean_var_plot (file)

PNG file; plot of the log-intensity variance vs log-intensity mean of each condition in the normalized samples

raw_dist_plot (file)

PNG file; plot of the intensity/ratio distributions of the raw samples

norm_dist_plot (file)

PNG file; plot of the intensity/ratio distributions of the normalized samples

raw_rdata (file)

RDS file of a proteinGroups object from Proteus, contains raw protein intensities and additional info

norm_rdata (file)

RDS file of a proteinGroups object from Proteus, contains normalized protein intensities and additional info

raw_tab (file)

TSV-format intensities table from Proteus, contains raw protein intensities

norm_tab (file)

TSV-format intensities table from Proteus, contains normalized protein intensities

session_info (file)

LOG file of the R sessionInfo from the module run

versions (file)

File containing software versions

versions.yml
included in
differentialabundance
maintainer
Github user WackerO
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