prepareSOFTfileForGEO {RnBeads} | R Documentation |
prepareSOFTfileForGEO
Description
Starting from an RnBeadSet
object generates a batch submission file for Gene Expression Omnibus series in SOFT format
Usage
prepareSOFTfileForGEO(
rnb.set,
filename,
sample.source.col = NULL,
sample.description.col = NULL,
sample.title.col = NULL,
export.cols = seq(ncol(pheno(rnb.set))),
rnb.set.raw = NULL,
sample.extra.info = NULL,
series.info = NULL
)
Arguments
rnb.set |
Object inheriting from class RnBeadSet
with "GSE" .
|
filename |
Absolute path or a name of a SOFT file to be generated
|
sample.source.col |
integer singleton specifying a column in the pheno slot of rnb.set
containing information which will be written into the field Sample_source_name_ch1
of each sample record
|
sample.description.col |
integer singleton specifying a column in the pheno slot of rnb.set
containing information which will be written into the field Sample_desription
of each sample record
|
sample.title.col |
integer singleton specifying a column in the pheno slot of rnb.set
containing information which will be written into the field Sample_title
of each sample record. If NULL , the result of samples(rnb.set) will be used
|
export.cols |
integer vector specifying columns in the pheno slot of rnb.set
containing information which will be written into the fields Sample_characteristics_ch1
of each sample record
|
rnb.set.raw |
Object inheriting from class RnBeadSet
|
sample.extra.info |
Optionally, a list with elements to be written to all series record. Elements should be character
singletons named with valid SOFT labels of a SAMPLE section, e.g.Sample_extract_protocol ,
Sample_hyb_protocol , Sample_label_protocol_ch1 , Sample_data_processing ,
Sample_contact_name , Sample_contact_email etc.
|
series.info |
A list with elements to be written to the series record. Elements should be character
singletons named SERIES (contains a valid GSE identifier for updating an existing series)
Series_title , Series_summary , Series_type , Series_overall_design ,
Series_contributor , Series_sample_id
|
Details
The code was largely adapted from a similar function in package lumi
which is due to Pan Du.
Value
TRUE
on success.
Author(s)
Pavlo Lutsik
[Package
RnBeads version 2.12.0
Index]