get_plates: use curatedTCGAData request to acquire plate codes for...
In BiocOncoTK: Bioconductor components for general cancer genomics
Description
Usage
Arguments
Value
Examples
Description
use curatedTCGAData request to acquire plate codes for samples
Usage
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get_plates(
tumcode = "BLCA",
assay = "RNASeq2GeneNorm",
samptypes = c("01", "02", "03", "04", "06", "09", "40")
)
Arguments
tumcode
a TCGA tumor code, usually 3 or for characters
assay
a curatedTCGAData assay code, run curatedTCGAData() to
see a message with available options
samptypes
a character vector with codes as
defined at https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/sample-type-codes
Value
a data.frame with a row for each TCGA contribution for the selected
tumor type and assay type
Examples
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if (interactive()) {
plts_blca_rnaseq = get_plates()
dim(plts_blca_rnaseq)
head(plts_blca_rnaseq)
}
BiocOncoTK documentation built on Nov. 8, 2020, 6:03 p.m.
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Description Usage Arguments Value Examples
Description
use curatedTCGAData request to acquire plate codes for samples
Usage
1 2 3 4 5 | get_plates(
tumcode = "BLCA",
assay = "RNASeq2GeneNorm",
samptypes = c("01", "02", "03", "04", "06", "09", "40")
)
|
Arguments
tumcode |
a TCGA tumor code, usually 3 or for characters |
assay |
a curatedTCGAData assay code, run curatedTCGAData() to see a message with available options |
samptypes |
a character vector with codes as defined at https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/sample-type-codes |
Value
a data.frame with a row for each TCGA contribution for the selected tumor type and assay type
Examples
1 2 3 4 5 | if (interactive()) {
plts_blca_rnaseq = get_plates()
dim(plts_blca_rnaseq)
head(plts_blca_rnaseq)
}
|
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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