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ShixiangWang/tcga_replicateFilter.R

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A R function used to Filter TCGA Replicate Samples
Raw
tcga_replicateFilter.R
#---------------------------------------------------
# Filter TCGA Replicate Samples
# Author: ShixiangWang <w_shixiang@163.com>
# ooooooo
# The filter rule following broad institute says:
#
# 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.
# oooooo
# Ref Link: <https://confluence.broadinstitute.org/display/GDAC/FAQ#FAQ-sampleTypesQWhatTCGAsampletypesareFirehosepipelinesexecutedupon>
#-------------------------------------------------------------------
tcga_replicateFilter = function(tsb, analyte_target=c("DNA","RNA"), decreasing=TRUE, analyte_position=20, plate=c(22,25), portion=c(18,19), filter_FFPE=FALSE, full_barcode=FALSE){
# basically, user provide tsb and analyte_target is fine. If you
# want to filter FFPE samples, please set filter_FFPE and full_barcode
# all to TRUE, and tsb must have nchar of 28
analyte_target = match.arg(analyte_target)
# Strings in R are largely lexicographic
# see ??base::Comparison
# filter FFPE samples
# provide by <http://gdac.broadinstitute.org/runs/sampleReports/latest/FPPP_FFPE_Cases.html>
if(full_barcode & filter_FFPE){
ffpe = c("TCGA-44-2656-01B-06D-A271-08", "TCGA-44-2656-01B-06D-A273-01",
"TCGA-44-2656-01B-06D-A276-05", "TCGA-44-2656-01B-06D-A27C-26",
"TCGA-44-2656-01B-06R-A277-07", "TCGA-44-2662-01B-02D-A271-08",
"TCGA-44-2662-01B-02D-A273-01", "TCGA-44-2662-01B-02R-A277-07",
"TCGA-44-2665-01B-06D-A271-08", "TCGA-44-2665-01B-06D-A273-01",
"TCGA-44-2665-01B-06D-A276-05", "TCGA-44-2665-01B-06R-A277-07",
"TCGA-44-2666-01B-02D-A271-08", "TCGA-44-2666-01B-02D-A273-01",
"TCGA-44-2666-01B-02D-A276-05", "TCGA-44-2666-01B-02D-A27C-26",
"TCGA-44-2666-01B-02R-A277-07", "TCGA-44-2668-01B-02D-A271-08",
"TCGA-44-2668-01B-02D-A273-01", "TCGA-44-2668-01B-02D-A276-05",
"TCGA-44-2668-01B-02D-A27C-26", "TCGA-44-2668-01B-02R-A277-07",
"TCGA-44-3917-01B-02D-A271-08", "TCGA-44-3917-01B-02D-A273-01",
"TCGA-44-3917-01B-02D-A276-05", "TCGA-44-3917-01B-02D-A27C-26",
"TCGA-44-3917-01B-02R-A277-07", "TCGA-44-3918-01B-02D-A271-08",
"TCGA-44-3918-01B-02D-A273-01", "TCGA-44-3918-01B-02D-A276-05",
"TCGA-44-3918-01B-02D-A27C-26", "TCGA-44-3918-01B-02R-A277-07",
"TCGA-44-4112-01B-06D-A271-08", "TCGA-44-4112-01B-06D-A273-01",
"TCGA-44-4112-01B-06D-A276-05", "TCGA-44-4112-01B-06D-A27C-26",
"TCGA-44-4112-01B-06R-A277-07", "TCGA-44-5645-01B-04D-A271-08",
"TCGA-44-5645-01B-04D-A273-01", "TCGA-44-5645-01B-04D-A276-05",
"TCGA-44-5645-01B-04D-A27C-26", "TCGA-44-5645-01B-04R-A277-07",
"TCGA-44-6146-01B-04D-A271-08", "TCGA-44-6146-01B-04D-A273-01",
"TCGA-44-6146-01B-04D-A276-05", "TCGA-44-6146-01B-04D-A27C-26",
"TCGA-44-6146-01B-04R-A277-07", "TCGA-44-6146-01B-04R-A27D-13",
"TCGA-44-6147-01B-06D-A271-08", "TCGA-44-6147-01B-06D-A273-01",
"TCGA-44-6147-01B-06D-A276-05", "TCGA-44-6147-01B-06D-A27C-26",
"TCGA-44-6147-01B-06R-A277-07", "TCGA-44-6147-01B-06R-A27D-13",
"TCGA-44-6775-01C-02D-A271-08", "TCGA-44-6775-01C-02D-A273-01",
"TCGA-44-6775-01C-02D-A276-05", "TCGA-44-6775-01C-02D-A27C-26",
"TCGA-44-6775-01C-02R-A277-07", "TCGA-44-6775-01C-02R-A27D-13",
"TCGA-A6-2674-01B-04D-A270-10", "TCGA-A6-2674-01B-04R-A277-07",
"TCGA-A6-2677-01B-02D-A270-10", "TCGA-A6-2677-01B-02D-A274-01",
"TCGA-A6-2677-01B-02D-A27A-05", "TCGA-A6-2677-01B-02D-A27E-26",
"TCGA-A6-2677-01B-02R-A277-07", "TCGA-A6-2684-01C-08D-A270-10",
"TCGA-A6-2684-01C-08D-A274-01", "TCGA-A6-2684-01C-08D-A27A-05",
"TCGA-A6-2684-01C-08D-A27E-26", "TCGA-A6-2684-01C-08R-A277-07",
"TCGA-A6-3809-01B-04D-A270-10", "TCGA-A6-3809-01B-04D-A274-01",
"TCGA-A6-3809-01B-04D-A27A-05", "TCGA-A6-3809-01B-04D-A27E-26",
"TCGA-A6-3809-01B-04R-A277-07", "TCGA-A6-3810-01B-04D-A270-10",
"TCGA-A6-3810-01B-04D-A274-01", "TCGA-A6-3810-01B-04D-A27A-05",
"TCGA-A6-3810-01B-04D-A27E-26", "TCGA-A6-3810-01B-04R-A277-07",
"TCGA-A6-5656-01B-02D-A270-10", "TCGA-A6-5656-01B-02D-A274-01",
"TCGA-A6-5656-01B-02D-A27A-05", "TCGA-A6-5656-01B-02D-A27E-26",
"TCGA-A6-5656-01B-02R-A277-07", "TCGA-A6-5656-01B-02R-A27D-13",
"TCGA-A6-5659-01B-04D-A270-10", "TCGA-A6-5659-01B-04D-A274-01",
"TCGA-A6-5659-01B-04D-A27A-05", "TCGA-A6-5659-01B-04D-A27E-26",
"TCGA-A6-5659-01B-04R-A277-07", "TCGA-A6-6650-01B-02D-A270-10",
"TCGA-A6-6650-01B-02D-A274-01", "TCGA-A6-6650-01B-02D-A27A-05",
"TCGA-A6-6650-01B-02D-A27E-26", "TCGA-A6-6650-01B-02R-A277-07",
"TCGA-A6-6650-01B-02R-A27D-13", "TCGA-A6-6780-01B-04D-A270-10",
"TCGA-A6-6780-01B-04D-A274-01", "TCGA-A6-6780-01B-04D-A27A-05",
"TCGA-A6-6780-01B-04D-A27E-26", "TCGA-A6-6780-01B-04R-A277-07",
"TCGA-A6-6780-01B-04R-A27D-13", "TCGA-A6-6781-01B-06D-A270-10",
"TCGA-A6-6781-01B-06D-A274-01", "TCGA-A6-6781-01B-06D-A27A-05",
"TCGA-A6-6781-01B-06R-A277-07", "TCGA-A6-6781-01B-06R-A27D-13",
"TCGA-A7-A0DB-01C-02D-A272-09", "TCGA-A7-A0DB-01C-02R-A277-07",
"TCGA-A7-A0DB-01C-02R-A27D-13", "TCGA-A7-A13D-01B-04D-A272-09",
"TCGA-A7-A13D-01B-04R-A277-07", "TCGA-A7-A13D-01B-04R-A27D-13",
"TCGA-A7-A13E-01B-06D-A272-09", "TCGA-A7-A13E-01B-06R-A277-07",
"TCGA-A7-A13E-01B-06R-A27D-13", "TCGA-A7-A26E-01B-06D-A272-09",
"TCGA-A7-A26E-01B-06D-A275-01", "TCGA-A7-A26E-01B-06D-A27B-05",
"TCGA-A7-A26E-01B-06R-A277-07", "TCGA-A7-A26E-01B-06R-A27D-13",
"TCGA-A7-A26J-01B-02D-A272-09", "TCGA-A7-A26J-01B-02D-A275-01",
"TCGA-A7-A26J-01B-02D-A27B-05", "TCGA-A7-A26J-01B-02D-A27F-26",
"TCGA-A7-A26J-01B-02R-A277-07", "TCGA-A7-A26J-01B-02R-A27D-13",
"TCGA-B2-3923-01B-10D-A270-10", "TCGA-B2-3923-01B-10R-A277-07",
"TCGA-B2-3923-01B-10R-A27D-13", "TCGA-B2-3924-01B-03D-A270-10",
"TCGA-B2-3924-01B-03D-A274-01", "TCGA-B2-3924-01B-03D-A27A-05",
"TCGA-B2-3924-01B-03D-A27E-26", "TCGA-B2-3924-01B-03R-A277-07",
"TCGA-B2-3924-01B-03R-A27D-13", "TCGA-B2-5633-01B-04D-A270-10",
"TCGA-B2-5633-01B-04D-A274-01", "TCGA-B2-5633-01B-04D-A27A-05",
"TCGA-B2-5633-01B-04D-A27E-26", "TCGA-B2-5633-01B-04R-A277-07",
"TCGA-B2-5633-01B-04R-A27D-13", "TCGA-B2-5635-01B-04D-A270-10",
"TCGA-B2-5635-01B-04D-A274-01", "TCGA-B2-5635-01B-04D-A27A-05",
"TCGA-B2-5635-01B-04D-A27E-26", "TCGA-B2-5635-01B-04R-A277-07",
"TCGA-B2-5635-01B-04R-A27D-13", "TCGA-BK-A0CA-01B-02D-A272-09",
"TCGA-BK-A0CA-01B-02D-A275-01", "TCGA-BK-A0CA-01B-02D-A27B-05",
"TCGA-BK-A0CA-01B-02D-A27F-26", "TCGA-BK-A0CA-01B-02R-A277-07",
"TCGA-BK-A0CA-01B-02R-A27D-13", "TCGA-BK-A0CC-01B-04D-A272-09",
"TCGA-BK-A0CC-01B-04D-A275-01", "TCGA-BK-A0CC-01B-04D-A27B-05",
"TCGA-BK-A0CC-01B-04R-A277-07", "TCGA-BK-A0CC-01B-04R-A27D-13",
"TCGA-BK-A139-01C-08D-A272-09", "TCGA-BK-A139-01C-08D-A275-01",
"TCGA-BK-A139-01C-08D-A27B-05", "TCGA-BK-A139-01C-08D-A27F-26",
"TCGA-BK-A139-01C-08R-A277-07", "TCGA-BK-A139-01C-08R-A27D-13",
"TCGA-BK-A26L-01C-04D-A272-09", "TCGA-BK-A26L-01C-04D-A275-01",
"TCGA-BK-A26L-01C-04D-A27B-05", "TCGA-BK-A26L-01C-04D-A27F-26",
"TCGA-BK-A26L-01C-04R-A277-07", "TCGA-BK-A26L-01C-04R-A27D-13",
"TCGA-BL-A0C8-01B-04D-A271-08", "TCGA-BL-A0C8-01B-04D-A273-01",
"TCGA-BL-A0C8-01B-04D-A276-05", "TCGA-BL-A0C8-01B-04D-A27C-26",
"TCGA-BL-A0C8-01B-04R-A277-07", "TCGA-BL-A0C8-01B-04R-A27D-13",
"TCGA-BL-A13I-01B-04D-A271-08", "TCGA-BL-A13I-01B-04D-A276-05",
"TCGA-BL-A13I-01B-04R-A277-07", "TCGA-BL-A13I-01B-04R-A27D-13",
"TCGA-BL-A13J-01B-04D-A271-08", "TCGA-BL-A13J-01B-04D-A273-01",
"TCGA-BL-A13J-01B-04D-A276-05", "TCGA-BL-A13J-01B-04D-A27C-26",
"TCGA-BL-A13J-01B-04R-A277-07", "TCGA-BL-A13J-01B-04R-A27D-13")
tsb = setdiff(tsb, tsb[which(tsb %in% ffpe)])
}
# find repeated samples
sampleID = substr(tsb, start = 1, stop = 15)
dp_samples = unique(sampleID[duplicated(sampleID)])
if(length(dp_samples)==0){
message("ooo Not find any duplicated barcodes, return original input..")
tsb
}else{
uniq_tsb = tsb[! sampleID %in% dp_samples]
dp_tsb = setdiff(tsb, uniq_tsb)
add_tsb = c()
# analyte = substr(dp_tsb, start = analyte_position, stop = analyte_position)
# if analyte_target = "DNA"
# analyte: D > G,W,X
if(analyte_target == "DNA"){
for(x in dp_samples){
mulaliquots = dp_tsb[substr(dp_tsb,1,15) == x]
analytes = substr(mulaliquots,
start = analyte_position,
stop = analyte_position)
if(any(analytes == "D") & !(all(analytes == "D"))){
aliquot = mulaliquots[which(analytes == "D")]
add_tsb = c(add_tsb, aliquot)
dp_tsb = setdiff(dp_tsb, mulaliquots)
}
}
}else{
for(x in dp_samples){
mulaliquots = dp_tsb[substr(dp_tsb,1,15) == x]
analytes = substr(mulaliquots,
start = analyte_position,
stop = analyte_position)
if(any(analytes == "H") & !(all(analytes == "H"))){
aliquot = mulaliquots[which(analytes == "H")]
add_tsb = c(add_tsb, aliquot)
dp_tsb = setdiff(dp_tsb, mulaliquots)
}else if(any(analytes == "R") & !(all(analytes == "R"))){
aliquot = mulaliquots[which(analytes == "R")]
add_tsb = c(add_tsb, aliquot)
dp_tsb = setdiff(dp_tsb, mulaliquots)
}else if(any(analytes == "T") & !(all(analytes == "T"))){
aliquot = mulaliquots[which(analytes == "T")]
add_tsb = c(add_tsb, aliquot)
dp_tsb = setdiff(dp_tsb, mulaliquots)
}
}
}
# if analyte_target = "RNA"
# analyte: H > R > T
# else{
#
# }
if(length(dp_tsb) == 0){
message("ooo Filter barcodes successfully!")
c(uniq_tsb, add_tsb)
}else{
# filter according to portion number
sampleID_res = substr(dp_tsb, start=1, stop=15)
dp_samples_res = unique(sampleID_res[duplicated(sampleID_res)])
for(x in dp_samples_res){
mulaliquots = dp_tsb[substr(dp_tsb,1,15) == x]
portion_codes = substr(mulaliquots,
start = portion[1],
stop = portion[2])
portion_keep = sort(portion_codes, decreasing = decreasing)[1]
if(!all(portion_codes == portion_keep)){
if(length(which(portion_codes == portion_keep)) == 1){
add_tsb = c(add_tsb, mulaliquots[which(portion_codes == portion_keep)])
dp_tsb = setdiff(dp_tsb, mulaliquots)
}else{
dp_tsb = setdiff(dp_tsb, mulaliquots[which(portion_codes != portion_keep)])
}
}
}
if(length(dp_tsb)==0){
message("ooo Filter barcodes successfully!")
c(uniq_tsb, add_tsb)
}else{
# filter according to plate number
sampleID_res = substr(dp_tsb, start=1, stop=15)
dp_samples_res = unique(sampleID_res[duplicated(sampleID_res)])
for(x in dp_samples_res){
mulaliquots = dp_tsb[substr(dp_tsb,1,15) == x]
plate_codes = substr(mulaliquots,
start = plate[1],
stop = plate[2])
plate_keep = sort(plate_codes, decreasing = decreasing)[1]
add_tsb = c(add_tsb, mulaliquots[which(plate_codes == plate_keep)])
dp_tsb = setdiff(dp_tsb, mulaliquots)
}
if(length(dp_tsb)==0){
message("ooo Filter barcodes successfully!")
c(uniq_tsb, add_tsb)
}else{
message("ooo barcodes ", dp_tsb, " failed in filter process, other barcodes will be returned.")
c(uniq_tsb, add_tsb)
}
}
}
}
}
#-------------------------
# Test and Check result
#------------------------
tsb = c("TCGA-55-7995-01A-11D-2183-01", "TCGA-55-8616-01A-11D-2389-01",
"TCGA-NJ-A4YG-01A-22D-A25M-01", "TCGA-44-2668-01A-01D-A273-01",
"TCGA-49-6761-01A-31D-1943-01", "TCGA-75-6207-01A-11D-1752-01",
"TCGA-73-4659-01A-01D-1204-01", "TCGA-78-7536-01A-11D-2062-01",
"TCGA-J2-8192-01A-11D-2237-01", "TCGA-49-AAR9-01A-21D-A40Z-01",
"TCGA-L4-A4E5-01A-11D-A24O-01", "TCGA-95-A4VK-01A-11D-A25M-01",
"TCGA-49-4486-01A-01D-1204-01", "TCGA-67-3772-01A-01D-0944-01",
"TCGA-78-7159-01A-11D-2035-01", "TCGA-55-A491-01A-11D-A24C-01",
"TCGA-05-4403-01A-01D-1204-01", "TCGA-97-8171-01A-11D-2283-01",
"TCGA-L4-A4E6-01A-11D-A24C-01", "TCGA-49-6743-01A-11D-1854-01",
"TCGA-62-8397-01A-11D-2322-01", "TCGA-MP-A4TF-01A-11D-A25M-01",
"TCGA-55-8207-01A-11D-2237-01", "TCGA-53-7813-01A-11D-2166-01",
"TCGA-44-7671-01A-11D-2062-01", "TCGA-78-7145-01A-11D-2035-01",
"TCGA-78-8655-01A-11D-2389-01", "TCGA-86-7955-01A-11D-2183-01",
"TCGA-4B-A93V-01A-11D-A396-01", "TCGA-MP-A4T6-01A-32D-A25M-01",
"TCGA-55-6986-01A-11D-1943-01", "TCGA-55-6981-01A-11D-1943-01",
"TCGA-97-8179-01A-11D-2283-01", "TCGA-44-5645-01A-01D-1624-01",
"TCGA-78-7537-01A-11D-2062-01", "TCGA-69-7760-01A-11D-2166-01",
"TCGA-55-6975-01A-11D-1943-01", "TCGA-49-6744-01A-11D-1854-01",
"TCGA-44-6776-01A-11D-1854-01", "TCGA-73-4677-01A-01D-1204-01",
"TCGA-75-7031-01A-11D-1943-01", "TCGA-55-7815-01A-11D-2166-01",
"TCGA-J2-A4AE-01A-21D-A24C-01", "TCGA-69-8253-01A-11D-2283-01",
"TCGA-38-6178-01A-11D-1752-01", "TCGA-55-8514-01A-11D-2389-01",
"TCGA-55-8508-01A-11D-2389-01", "TCGA-91-6828-01A-11D-1854-01",
"TCGA-78-7149-01A-11D-2035-01", "TCGA-64-5779-01A-01D-1624-01",
"TCGA-62-8399-01A-21D-2322-01", "TCGA-44-6779-01A-11D-1854-01",
"TCGA-49-6745-01A-11D-1854-01", "TCGA-44-5643-01A-01D-1624-01",
"TCGA-62-A46U-01A-11D-A24C-01", "TCGA-55-8506-01A-11D-2389-01",
"TCGA-44-A4SU-01A-11D-A24O-01", "TCGA-55-8301-01A-11D-2283-01",
"TCGA-05-5425-01A-02D-1624-01", "TCGA-55-8619-01A-11D-2389-01",
"TCGA-86-A4P7-01A-11D-A24O-01", "TCGA-55-8208-01A-11D-2237-01",
"TCGA-05-4398-01A-01D-1204-01", "TCGA-55-7728-01A-11D-2183-01",
"TCGA-49-AAR0-01A-21D-A396-01", "TCGA-44-3398-01A-01D-1549-01",
"TCGA-78-7540-01A-11D-2062-01", "TCGA-64-5815-01A-01D-1624-01",
"TCGA-62-A46Y-01A-11D-A24C-01", "TCGA-53-7624-01A-11D-2062-01",
"TCGA-73-4676-01A-01D-1752-01", "TCGA-62-8395-01A-11D-2322-01",
"TCGA-55-6985-01A-11D-1943-01", "TCGA-49-AARO-01A-12D-A40Z-01",
"TCGA-95-7567-01A-11D-2062-01", "TCGA-75-5126-01A-01D-1752-01",
"TCGA-86-7954-01A-11D-2183-01", "TCGA-86-7701-01A-11D-2166-01",
"TCGA-NJ-A4YP-01A-11D-A25M-01", "TCGA-95-7562-01A-11D-2237-01",
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"TCGA-MP-A4T9-01A-11D-A24O-01", "TCGA-78-7143-01A-11D-2035-01",
"TCGA-44-7659-01A-11D-2062-01", "TCGA-75-7025-01A-12D-1943-01",
"TCGA-44-6147-01A-11D-1752-01", "TCGA-62-8394-01A-11D-2322-01",
"TCGA-80-5607-01A-31D-1943-01", "TCGA-44-8120-01A-11D-2237-01",
"TCGA-69-7978-01A-11D-2183-01", "TCGA-91-7771-01A-11D-2166-01",
"TCGA-44-2665-01B-06D-A273-01", "TCGA-86-8279-01A-11D-2283-01",
"TCGA-97-A4M3-01A-11D-A24O-01", "TCGA-73-4658-01A-01D-1752-01",
"TCGA-55-1592-01A-01D-0944-01", "TCGA-55-8205-01A-11D-2237-01",
"TCGA-86-6851-01A-11D-1943-01", "TCGA-55-8097-01A-11D-2237-01",
"TCGA-86-8359-01A-11D-2322-01", "TCGA-64-1679-01A-21D-2062-01",
"TCGA-86-7711-01A-11D-2062-01", "TCGA-55-7281-01A-11D-2035-01",
"TCGA-44-2666-01A-01D-0944-01", "TCGA-44-2656-01A-02D-A273-01",
"TCGA-55-8615-01A-11D-2389-01", "TCGA-J2-A4AD-01A-11D-A24C-01",
"TCGA-75-5146-01A-01D-1624-01", "TCGA-38-7271-01A-11D-2035-01",
"TCGA-55-7227-01A-11D-2035-01", "TCGA-93-A4JQ-01A-11D-A24O-01",
"TCGA-44-7672-01A-11D-2062-01", "TCGA-55-6979-01A-11D-1943-01",
"TCGA-86-6562-01A-11D-1752-01", "TCGA-MP-A4TJ-01A-51D-A25M-01",
"TCGA-99-8025-01A-11D-2237-01", "TCGA-38-4628-01A-01D-1204-01",
"TCGA-05-4424-01A-22D-1854-01", "TCGA-97-8176-01A-11D-2389-01",
"TCGA-97-8175-01A-11D-2283-01", "TCGA-55-7911-01A-11D-2166-01",
"TCGA-05-4434-01A-01D-1204-01", "TCGA-44-6146-01A-11D-A273-01",
"TCGA-73-4668-01A-01D-1204-01", "TCGA-86-8054-01A-11D-2237-01",
"TCGA-50-5044-01A-21D-1854-01", "TCGA-44-6778-01A-11D-1854-01",
"TCGA-62-A46R-01A-11D-A24C-01", "TCGA-44-3917-01B-02D-A273-01",
"TCGA-78-7542-01A-21D-2062-01", "TCGA-64-1681-01A-11D-2062-01",
"TCGA-91-6848-01A-11D-1943-01", "TCGA-55-8513-01A-11D-2389-01",
"TCGA-L9-A7SV-01A-11D-A396-01", "TCGA-49-AAQV-01A-11D-A396-01",
"TCGA-49-AAR2-01A-11D-A396-01", "TCGA-44-4112-01A-01D-1877-01",
"TCGA-05-4410-01A-21D-1854-01", "TCGA-MP-A4TH-01A-31D-A25M-01",
"TCGA-55-A4DF-01A-11D-A24C-01", "TCGA-78-7162-01A-21D-2062-01",
"TCGA-44-5644-01A-21D-2035-01", "TCGA-73-A9RS-01A-11D-A40Z-01",
"TCGA-55-A490-01A-11D-A24C-01", "TCGA-55-8091-01A-11D-2237-01",
"TCGA-49-AAR4-01A-12D-A40Z-01", "TCGA-78-7146-01A-11D-2035-01",
"TCGA-95-A4VP-01A-21D-A25M-01", "TCGA-93-7348-01A-21D-2035-01",
"TCGA-69-8254-01A-11D-2283-01", "TCGA-44-7662-01A-11D-2062-01",
"TCGA-78-8662-01A-11D-2389-01", "TCGA-44-3918-01B-02D-A273-01",
"TCGA-91-A4BD-01A-11D-A24C-01", "TCGA-95-7947-01A-11D-2183-01",
"TCGA-55-A48Z-01A-12D-A24O-01", "TCGA-49-4512-01A-21D-1854-01",
"TCGA-73-4662-01A-01D-1204-01", "TCGA-50-5072-01A-21D-1854-01",
"TCGA-95-A4VN-01A-11D-A25M-01", "TCGA-55-1596-01A-01D-0944-01",
"TCGA-44-A47B-01A-11D-A24C-01", "TCGA-97-A4M0-01A-11D-A24O-01",
"TCGA-44-6148-01A-11D-1752-01", "TCGA-55-7903-01A-11D-2166-01",
"TCGA-50-6593-01A-11D-1752-01", "TCGA-L9-A8F4-01A-11D-A396-01",
"TCGA-55-7994-01A-11D-2183-01", "TCGA-L9-A5IP-01A-21D-A396-01",
"TCGA-55-6982-01A-11D-1943-01", "TCGA-44-8117-01A-11D-2237-01",
"TCGA-50-5935-01A-11D-1752-01", "TCGA-78-7154-01A-11D-2035-01",
"TCGA-99-7458-01A-11D-2035-01", "TCGA-62-A471-01A-12D-A24C-01",
"TCGA-50-6590-01A-12D-1854-01", "TCGA-91-6835-01A-11D-1854-01",
"TCGA-44-6144-01A-11D-1752-01", "TCGA-73-4675-01A-01D-1204-01",
"TCGA-50-7109-01A-11D-2035-01", "TCGA-55-7913-01B-11D-2237-01"
)
# Sort replicate filter
require(tidyverse)
tsb %>% substr(1,15) %>% unique() -> test_tsb
uniq_tsb = tcga_replicateFilter(tsb = tsb)
all(test_tsb %in% substr(uniq_tsb, 1, 15))
all.equal(sort(test_tsb), sort(substr(uniq_tsb, 1, 15)))
# DNA analyte replicate filter
tcga_replicateFilter(tsb = c("TCGA-55-7913-01B-11D-2237-01", "TCGA-55-7913-01B-11X-2237-01", "TCGA-55-7913-01B-11D-2237-01"))
# RNA analyte replicate filter
tcga_replicateFilter(tsb = c("TCGA-55-7913-01B-11H-2237-01", "TCGA-55-7913-01B-11R-2237-01", "TCGA-55-7913-01B-11T-2237-01"), analyte_target = "RNA")
tcga_replicateFilter(tsb = c("TCGA-55-7913-01B-11R-2237-01", "TCGA-55-7913-01B-11R-2237-01", "TCGA-55-7913-01B-11T-2237-01"), analyte_target = "RNA")
tcga_replicateFilter(tsb = c("TCGA-55-7913-01B-11T-2237-01", "TCGA-55-7913-01B-11T-2237-01", "TCGA-55-7913-01B-11D-2237-01"), analyte_target = "RNA")
####### test result
#> all(test_tsb %in% substr(uniq_tsb, 1, 15))
#[1] TRUE
#> all.equal(sort(test_tsb), sort(substr(uniq_tsb, 1, 15)))
#[1] TRUE
#> # DNA analyte replicate filter
#> tcga_replicateFilter(tsb = c("TCGA-55-7913-01B-11D-2237-01", "TCGA-55-7913-01B-11X-2237-01", "TCGA-55-7913-01B-11D-2237-01"))
#ooo Filter barcodes successfully!
#[1] "TCGA-55-7913-01B-11D-2237-01"
#> # RNA analyte replicate filter
#> tcga_replicateFilter(tsb = c("TCGA-55-7913-01B-11H-2237-01", "TCGA-55-7913-01B-11R-2237-01", "TCGA-55-7913-01B-11T-2237-01"), analyte_target = "RNA")
#ooo Filter barcodes successfully!
#[1] "TCGA-55-7913-01B-11H-2237-01"
#> tcga_replicateFilter(tsb = c("TCGA-55-7913-01B-11R-2237-01", "TCGA-55-7913-01B-11R-2237-01", "TCGA-55-7913-01B-11T-2237-01"), analyte_target = "RNA")
#ooo Filter barcodes successfully!
#[1] "TCGA-55-7913-01B-11R-2237-01"
#> tcga_replicateFilter(tsb = c("TCGA-55-7913-01B-11T-2237-01", "TCGA-55-7913-01B-11T-2237-01", "TCGA-55-7913-01B-11D-2237-01"), analyte_target = "RNA")
#ooo Filter barcodes successfully!
#[1] "TCGA-55-7913-01B-11T-2237-01"
## filter FFPE samples, provied in <http://gdac.broadinstitute.org/runs/sampleReports/latest/FPPP_FFPE_Cases.html>
## please note
# basically, user provide tsb and analyte_target is fine. If you
# want to filter FFPE samples, please set filter_FFPE and full_barcode
# all to TRUE, and tsb must have nchar of 28
# > tcga_replicateFilter(tsb = c("TCGA-55-7913-01B-11H-2237-01", "TCGA-55-7913-01B-11R-2237-01", "TCGA-55-7913-01B-11T-2237-01", "TCGA-44-2656-01B-06D-A271-08", "TCGA-44-2656-01B-06D-A273-01"), analyte_target = "RNA")
# ooo Filter barcodes successfully!
# [1] "TCGA-55-7913-01B-11H-2237-01" "TCGA-44-2656-01B-06D-A273-01"
# > tcga_replicateFilter(tsb = c("TCGA-55-7913-01B-11H-2237-01", "TCGA-55-7913-01B-11R-2237-01", "TCGA-55-7913-01B-11T-2237-01", "TCGA-44-2656-01B-06D-A271-08", "TCGA-44-2656-01B-06D-A273-01"), analyte_target = "RNA", filter_FFPE = TRUE, full_barcode = TRUE)
# ooo Filter barcodes successfully!
# [1] "TCGA-55-7913-01B-11H-2237-01"
@ShixiangWang
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@Lesdormis Yes it can be also used.

@ShaowenJ
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Thanks!

@talipzengin
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Hi @ShixiangWang,
I have a patient who has RNA samples from two different vials after running this code. I need extra filtering for vials in this code. Which vial should I choose? A or B? Can I modify your code? Thanks in advance.

@ShixiangWang
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you can check ref link. Modify is of course allowed.

@ndaniel
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ndaniel commented Oct 30, 2023

It looks like some ids are still missing from the FFPE list, like for example TCGA-AC-A2QH-01B-04R-A22O-07 which is mentioned here as FFPE sample https://gdac.broadinstitute.org/runs/analyses__2016_01_28/samples_report/BRCA_FFPE_Cases.html .

@ShixiangWang
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@ndaniel Thank you for providing the supplementary message.

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