prepareSOFTfileForGEO: prepareSOFTfileForGEO

In RnBeads: RnBeads

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

RnBeads documentation built on March 3, 2021, 2 a.m.