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Filter TCGA Replicate Sample Barcodes

Source: R/tcga_barcodes.R
filter_tcga_barcodes.Rd

Check details for filter rules.

Usage

filter_tcga_barcodes(
  tsb,
  analyte_target = c("DNA", "RNA"),
  decreasing = TRUE,
  analyte_position = 20,
  plate = c(22, 25),
  portion = c(18, 19),
  filter_FFPE = FALSE
)

Arguments

tsb

a vector of TCGA sample barcodes.

analyte_target

type of barcodes, "DNA" or "RNA".

decreasing

if TRUE (default), use decreasing order to select barcode to keep.

analyte_position

bit position for analyte. DON'T CHANGE IT if you don't understand.

plate

bit position for plate. DON'T CHANGE IT if you don't understand.

portion

bit position for portion. DON'T CHANGE IT if you don't understand.

filter_FFPE

if TRUE (FALSE is default), filter out FFPE samples.

Value

a barcode list.

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. Two filters are applied to achieve this aim: an Analyte Replicate Filter and a Sort Replicate Filter.

Analyte Replicate Filter

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.

Sort Replicate Filter

The following precedence rules are applied when the analyte filter still produces more than one sample. The sort filter chooses the aliquot with the highest lexicographical sort value, to ensure that the barcode with the highest portion and/or plate number is selected when all other barcode fields are identical.

NOTE: Basically, user provides tsb and analyte_target is fine.

References

Rules:

  • https://confluence.broadinstitute.org/display/GDAC/FAQ#FAQ-sampleTypesQWhatTCGAsampletypesareFirehosepipelinesexecutedupon

FFPE cases:

  • http://gdac.broadinstitute.org/runs/sampleReports/latest/FPPP_FFPE_Cases.html

Examples

filter_tcga_barcodes(c("TCGA-44-2656-01B-06D-A271-08", "TCGA-44-2656-01B-06D-A273-01"))
#> ooo Filter barcodes successfully!
#> [1] "TCGA-44-2656-01B-06D-A273-01"
filter_tcga_barcodes(c("TCGA-44-2656-01B-06D-A271-08", "TCGA-44-2656-01B-06D-A273-01"),
  filter_FFPE = TRUE
)
#> ooo Not find any duplicated barcodes, return..
#> character(0)