sampleSheet: Read a Sample sheet for a BeadArray experiment
In markdunning/beadarray-devel: Quality assessment and low-level analysis for Illumina BeadArray data
Description
Usage
Arguments
Details
Value
Author(s)
Description
Read a comma-separated sample sheet into beadarray, which can then be used to annotate the data that beadarray reads in and add relevant metadata to the analysis.
Usage
1
readSampleSheet(sheet = "sampleSheet.csv")
Arguments
sheet
A file name for the sample sheet
Details
The sample sheet should describe all sections are expected to be part of the experiment, along with any relevant metadata. We assume the GenomeStudio sample sheet specification, with [Data] and [Header] sections. The Data section is where the sample metadata are defined. One row is required for each section, and the columns Sentrix\_ID, Sentrix\_Position, Sample\_Name, Sample\_Group must be present. The Sentrix\_ID and Sentrix\_Position columns give the name of the chip (usually a 10 digit number) and slot (a letter A to L) where a given sample was hybridised to. The Sample\_Group and Sample\_Name columns can take any valid R name. If there are muliple images per section, for example for Mouse WG-6 data, which have bead-level data suffixed by A\_1, A\_2, B\_1, B\_2 etc, only one entry is required in the sample sheet for sections A and B. beadarray will duplicate the metadata as neccessary.
Value
a list comprised of a tabular sample table and any header information that is present.
Author(s)
Mark Dunning
markdunning/beadarray-devel documentation built on May 21, 2019, noon
R Package Documentation
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Description Usage Arguments Details Value Author(s)
Description
Read a comma-separated sample sheet into beadarray, which can then be used to annotate the data that beadarray reads in and add relevant metadata to the analysis.
Usage
1 | readSampleSheet(sheet = "sampleSheet.csv")
|
Arguments
sheet |
A file name for the sample sheet |
Details
The sample sheet should describe all sections are expected to be part of the experiment, along with any relevant metadata. We assume the GenomeStudio sample sheet specification, with [Data] and [Header] sections. The Data section is where the sample metadata are defined. One row is required for each section, and the columns Sentrix\_ID, Sentrix\_Position, Sample\_Name, Sample\_Group must be present. The Sentrix\_ID and Sentrix\_Position columns give the name of the chip (usually a 10 digit number) and slot (a letter A to L) where a given sample was hybridised to. The Sample\_Group and Sample\_Name columns can take any valid R name. If there are muliple images per section, for example for Mouse WG-6 data, which have bead-level data suffixed by A\_1, A\_2, B\_1, B\_2 etc, only one entry is required in the sample sheet for sections A and B. beadarray will duplicate the metadata as neccessary.
Value
a list comprised of a tabular sample table and any header information that is present.
Author(s)
Mark Dunning
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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