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 2.10.0 Index]