read_idat: Read Illumina 450k methylation array IDATs specified in a...
In kevinlul/EpigeneLite: Lite version of EpigenCentral
Description
Usage
Arguments
Details
Value
References
Examples
Description
A sample sheet is a CSV with at least the following columns:
Sample_Name, Sample_Group, Sentrix_ID, Sentrix_Position
Further columns may annotate with other metadata about the samples for
other types of analysis not performed by this package.
Usage
1
read_idat(csv_sample_sheet_file)
Arguments
csv_sample_sheet_file
Path to a CSV sample sheet
Details
Sample_Name should be unique. Sample_Group should be either "control" or the
name of a case type, which will be used to differentiate the classes when
finding differentially methylated CpGs.
paste(Sample_Name, Sentrix_ID, Sentrix_Position, sep = "_") should result in
a prefix of the filenames of the corresponding red and green channel IDATs.
An example for the GSE55491 dataset of Silver Russel syndrome patients is
in extdata/
Value
normalized minfi GenomicRatioSet
References
Prickett AR, Ishida M, Böhm S, Frost JM et al. Genome-wide methylation analysis
in Silver-Russell syndrome patients. Hum Genet 2015 Mar;134(3):317-332. PMID: 25563730
Examples
1
2
3
4
## Not run:
grset <- read_idat("extdata/GSE55491/samplesheet.rss-GSE55491.csv")
## End(Not run)
kevinlul/EpigeneLite documentation built on Dec. 21, 2021, 6:35 a.m.
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Description Usage Arguments Details Value References Examples
Description
A sample sheet is a CSV with at least the following columns: Sample_Name, Sample_Group, Sentrix_ID, Sentrix_Position Further columns may annotate with other metadata about the samples for other types of analysis not performed by this package.
Usage
1 | read_idat(csv_sample_sheet_file)
|
Arguments
csv_sample_sheet_file |
Path to a CSV sample sheet |
Details
Sample_Name should be unique. Sample_Group should be either "control" or the name of a case type, which will be used to differentiate the classes when finding differentially methylated CpGs.
paste(Sample_Name, Sentrix_ID, Sentrix_Position, sep = "_") should result in a prefix of the filenames of the corresponding red and green channel IDATs.
An example for the GSE55491 dataset of Silver Russel syndrome patients is in extdata/
Value
normalized minfi GenomicRatioSet
References
Prickett AR, Ishida M, Böhm S, Frost JM et al. Genome-wide methylation analysis in Silver-Russell syndrome patients. Hum Genet 2015 Mar;134(3):317-332. PMID: 25563730
Examples
1 2 3 4 | ## Not run:
grset <- read_idat("extdata/GSE55491/samplesheet.rss-GSE55491.csv")
## End(Not run)
|
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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