tcga_remove_duplicated_samples: remove duplicated samples in TCGA
In Yunuuuu/yjtools: Toolkit for Yun and Jin (yjtools),
tcga_remove_duplicated_samples R Documentation
remove duplicated samples in TCGA
Description
remove duplicated samples in TCGA based on Firehose principle
Usage
tcga_remove_duplicated_samples(barcode)
Arguments
barcode
a character vector gives barcode of TCGA
Details
In many instances there is more than one aliquot for a given
combination of individual, platform, and data type. However, only one
aliquot may be ingested into Firehose. Therefore, a set of precedence rules
are applied to select the most scientifically advantageous one among them.
The following precedence rules are applied when the aliquots have differing
analytes. For RNA aliquots, T analytes are dropped in preference to H and R
analytes, since T is the inferior extraction protocol. If H and R are
encountered, H is the chosen analyte. This is somewhat arbitrary and
subject to change, since it is not clear at present whether H or R is the
better protocol. If there are multiple aliquots associated with the chosen
RNA analyte, the aliquot with the later plate number is chosen. For DNA
aliquots, D analytes (native DNA) are preferred over G, W, or X
(whole-genome amplified) analytes, unless the G, W, or X analyte sample has
a higher plate number.
Value
a tibble with duplicated barcode removed
Author(s)
References
Yunuuuu/yjtools documentation built on Jan. 29, 2024, 5:30 a.m.
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| tcga_remove_duplicated_samples | R Documentation |
remove duplicated samples in TCGA
Description
remove duplicated samples in TCGA based on Firehose principle
Usage
tcga_remove_duplicated_samples(barcode)
Arguments
barcode |
a character vector gives barcode of TCGA |
Details
In many instances there is more than one aliquot for a given combination of individual, platform, and data type. However, only one aliquot may be ingested into Firehose. Therefore, a set of precedence rules are applied to select the most scientifically advantageous one among them.
The following precedence rules are applied when the aliquots have differing analytes. For RNA aliquots, T analytes are dropped in preference to H and R analytes, since T is the inferior extraction protocol. If H and R are encountered, H is the chosen analyte. This is somewhat arbitrary and subject to change, since it is not clear at present whether H or R is the better protocol. If there are multiple aliquots associated with the chosen RNA analyte, the aliquot with the later plate number is chosen. For DNA aliquots, D analytes (native DNA) are preferred over G, W, or X (whole-genome amplified) analytes, unless the G, W, or X analyte sample has a higher plate number.
Value
a tibble with duplicated barcode removed
Author(s)
References
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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