mitch_calc: mitch_calc

Description Usage Arguments Value Examples

View source: R/mitch.R

Description

This function performs multivariate gene set enrichment analysis.

Usage

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mitch_calc(
  x,
  genesets,
  minsetsize = 10,
  cores = detectCores() - 1,
  resrows = 50,
  priority = NULL
)

Arguments

x

a multicolumn numerical table with each column containing differential expression scores for a contrast. Rownames must match genesets.

genesets

lists of genes imported by the gmt_imprt function or similar.

minsetsize

the minimum number of genes required in a set for it to be included in the statistical analysis. Default is 10.

cores

the number of parallel threads for computation. Defaults to the number of cores present minus 1.

resrows

an integer value representing the number of top genesets for which a detailed report is to be generated. Default is 50.

priority

the prioritisation metric used to selecting top gene sets. Valid options are 'significance', 'effect' and 'SD'.

Value

mitch res object with the following parts: $input_profile: the supplied input differential profile $input_genesets: the supplied input gene sets $ranked_profile: the differential profile after ranking $enrichment_result: the table of MANOVA/ANOVA enrichment results for each gene set $analysis_metrics: several metrics that are important to the interpretation of the results $detailed_sets: a list of dataframes containing ranks of members of prioritised gene sets.

Examples

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# Example using mitch to calculate multivariate enrichments and
# prioritise based on effect size 
data(myImportedData,genesetsExample)
resExample<-mitch_calc(myImportedData,genesetsExample,priority='effect',
minsetsize=5,cores=2)

mitch documentation built on Nov. 8, 2020, 6 p.m.