ezcamerapr: A wrapper function for 'cameraPR' with output to Excel
In jdreyf/ezlimma: Streamlines and extends limma package

ezcamerapr

R Documentation

A wrapper function for `cameraPR` with output to Excel

Description

Test whether a set of genes is highly ranked relative to other genes in terms of differential expression, accounting for inter-gene correlation with cameraPR. To find pathways whose genes have large magnitude changes, independent of direction of their change, provide abs of gene stats, and set alternative="Up". It returns a data frame with statistics per gene set, and writes this to an Excel file. The Excel file links to CSV files, which contain statistics per gene set.

Usage

ezcamerapr(
  stats.tab,
  G,
  feat.tab,
  name = NA,
  adjust.method = "BH",
  alternative = c("two.sided", "greater", "less", "Up", "Down"),
  min.nfeats = 3,
  max.nfeats = 1000,
  inter.gene.cor = 0.01,
  pwy.nchar = 199
)

Arguments

`stats.tab`	A matrix-like data object with gene row names & named columns of numeric gene-wise statistics (e.g. z-scores, t-statistics) by which genes can be ranked. The row names should be the same as the row names of `feat.tab`. All values must be `finite`.
`G`	Gene set list as returned from `read_gmt`.
`feat.tab`	Table of feature (e.g. gene) statistics that the Excel table can link to.
`name`	Name for the folder and Excel file that get written. Set to `NA` to avoid writing output.
`adjust.method`	Method used to adjust the p-values for multiple testing. Only for `mroast`.
`alternative`	Alternative hypothesis; must be one of`"two.sided"`; `"greater"` or `"less"`, or their synonyms `"Up"` or `"Down"`.
`min.nfeats`	Minimum number of features (e.g. genes) needed in a gene set for testing.
`max.nfeats`	Maximum number of features (e.g. genes) needed in a gene set for testing.
`inter.gene.cor`	Numeric inter-gene correlation within tested sets. Can be estimated with `interGeneCorrelation`.
`pwy.nchar`	Numeric maximum number of characters allowed in pathway name.