summarizeGEOSoft: summarize GEOSoft probes

In raim/segmenTools: Tools for Functional Genome Exploration

summarize GEOSoft probes

Description

takes as input the list returned by parseGEOSoft, a GEO microarray data set, including a table of probe mappings, as provided via GEO soft family files. Argument id specifies a probe mapping column ID. Multiples probes for the same features (same string in column ID) will then be summarized by the function in argument avg (default: median). If the package farms installed, the more sophisticated probe summarization of this package can be used https://www.bioconductor.org/packages/release/bioc/html/farms.html.

Usage

summarizeGEOSoft(
  data,
  id = "ORF",
  avg = "mean",
  farms = FALSE,
  keep.empty = FALSE,
  replicate = FALSE,
  repsep = ";",
  verb = TRUE,
  ...
)

Arguments

data	a list as returned by function parseGEOSoft
id	a column ID; probes with equal strings in this column will be summarized
avg	a function (or the name of a function as a string) for calculating an ‘average’ value for each cluster; default is the mean
farms	logical to indicate to use the bioconductor package farms for probe summarization (function generateExprVal.method.farms)
keep.empty	keep columns with no entry in column ID by copying the probe ID
replicate	if TRUE probe sets assigned to multiple features (separated by string provided in rep.sep) will be duplicated to and each feature will get its own row
repsep	separator for multiple-feature probes
verb	print messages
...	arguments to the function specified in avg or for function generateExprVal.method.farms if farms==TRUE

See Also

parseGEOSoft

raim/segmenTools documentation built on April 25, 2024, 10:14 a.m.