read.group.file: Read group file

In fboulnois/made: Microarray Analysis of Differential Expression

Description

Read and validate the group file associated with a microarray experiment.

Usage

read.group.file(config)

Arguments

config

Character string consisting of the path to the configuration file generated using the write.yaml.config function or parsed configuration list associated with a microarray experiment.

Details

Note: This function is mostly for internal use. Users should use read.yaml.config instead because it calls this function by default.

The group file describes which samples belong to which groups or conditions, for example normal controls and experimental cases. Groups must be assigned prior to launching the analysis. Groups are compared according to the option contrast_groups in the configuration and can be defined at three different levels:

"dirs"

Each directory containing samples can be assigned a group.

"files"

Each individual sample can be assigned a group.

"eset"

Each sample specified in an expression set can be assigned a group.

Value

Returns a modified configuration with group data.

See Also

write.yaml.config to generate the configuration file and read.yaml.config to read and validate it.

Examples

if(require(madeData))
{
  config <- system.file("extdata", "config.yaml", package = "madeData")
  read.group.file(config)
}

fboulnois/made documentation built on May 16, 2019, 12:01 p.m.