read_geo_tsv: Parse tab-delimited methylation matrices often found in GEO...
In kevinlul/EpigeneLite: Lite version of EpigenCentral
Description
Usage
Arguments
Value
References
Examples
Description
This is meant to parse the uncompressed Series Matrix files when IDATs
are not available. A CSV sample sheet of the same format required by read_idat
should still be provided to annotate Sample_Group for analysis, otherwise
you will only be able to generate PCA plots.
Usage
1
read_geo_tsv(tsv_beta_matrix_file, csv_sample_sheet_file = NULL)
Arguments
tsv_beta_matrix_file
Path to the GEO text file
csv_sample_sheet_file
Path to the sample sheet for annotations. Optional
Value
parsed 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_geo_tsv("extdata/GSE55491/GSE55491_series_matrix.txt")
## End(Not run)
kevinlul/EpigeneLite documentation built on Dec. 21, 2021, 6:35 a.m.
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Description Usage Arguments Value References Examples
Description
This is meant to parse the uncompressed Series Matrix files when IDATs are not available. A CSV sample sheet of the same format required by read_idat should still be provided to annotate Sample_Group for analysis, otherwise you will only be able to generate PCA plots.
Usage
1 | read_geo_tsv(tsv_beta_matrix_file, csv_sample_sheet_file = NULL)
|
Arguments
tsv_beta_matrix_file |
Path to the GEO text file |
csv_sample_sheet_file |
Path to the sample sheet for annotations. Optional |
Value
parsed 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_geo_tsv("extdata/GSE55491/GSE55491_series_matrix.txt")
## 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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