write.yaml.config: Write YAML configuration
In fboulnois/made: Microarray Analysis of Differential Expression

Description Usage Arguments Details Value See Also Examples

Generate the configuration file describing a microarray experiment.

1	write.yaml.config(analysisDir, groupBy = NULL, ...)

`analysisDir`	Character string consisting of the path to the analysis directory.
`groupBy`	Must be one of `"dirs"`, `"files"`, or `"eset"`.
`...`	Additional options to pass to the function.

Generates the configuration and group file which describe a reproducible microarray experiment. The files are created in the analysis directory using the analysisDir option. The group file describes which samples belong to which groups or conditions, for example normal controls and experimental cases. The user must specify at which level they are grouping their samples using the groupBy option:

"dirs": Each directory containing samples can be assigned a group. This option is useful if there are many samples in the experiment. If this option is specified, before running this function the analysis directory must already contain subdirectories of samples.
"files": Each individual sample can be assigned a group. If this option is specified, before running this function the analysis directory must already contain samples.
"eset": Each sample specified in an expression set can be assigned a group. If this option is specified, the expression set must also be passed as an additional argument to the function.

Other configuration options can also be specified as additional arguments, otherwise defaults will be used:

qvalue

A number between 0 and 1 which corrects the pvalue for multiple comparisons and describes the minimum false discovery rate (FDR) at which a test may be called significant: the default is 0.05.

adjust.batch.effect

A logical indicating whether or not batch effects should be adjusted: the default is TRUE.

save.intermediates

A logical indicating whether or not intermediate outputs should be saved: the default is FALSE.

quality.assessment

A logical indicating whether or not quality assessment should be performed: the default is TRUE.

normalization

Either "rma", TRUE, or FALSE, indicating what sort of background correction and normalization should be performed, if any. Setting this value to FALSE is useful for quality assessment, since the expression set will not be background corrected or normalized: the default is "rma".

summarization

A logical indicating whether or not gene level summarization should be performed: the default is TRUE.

write.report

A logical indicating whether or not a report of the experiment should be created: the default is TRUE.

group.file

A character string describing the name to give the group file: the default is to name the file "groups.txt".

contrast.groups

A character string of one or more formulas separated by a comma describing how the different groups should be compared: by default groups "A", "B", and "C" are created and are each compared to each other.

eset

An expression set object describing the microarray experiment at the level of probes. This option should only be used if the groupBy option is set to "eset", and thus has no default.

groups.df

A data.frame indicating which samples belong to which groups.

This option has no default: it can be used to programmatically set the groups for each sample ahead of time, otherwise the user will need to modify the group file after the configuration has been created.

A character string consisting of the path to the configuration file.

read.yaml.config to read and validate the configuration.

if(require(madeData))
{
  dataPath <- system.file("extdata", package = "madeData")
  write.yaml.config(dataPath, groupBy = "dirs")
}
write.yaml.config(getwd(), groupBy = "files", qvalue = 0.01)
write.yaml.config(getwd(), groupBy = "eset", eset = eset)