Question

I have a for loop that is awfully slow and doesnt work proper, it looks in 1 data.frame for a barcode and than searches for that barcode in another data.frame. The bar_code of the 2nd data.frame can be there multiple times. Every time it finds a barcode a counter should count the amount of times the barcode is there and write the number of barcodes to the 1st data frame.

My try:

for(i in 1:length(tcgadataUniek$Tumor_Sample_Barcode)){
  for(j in 1:length(hprdDataSorted$Samples.Int1)){
  count<-0
  if(i==j){
    count<-count+1
  } else {
    count<-count+0
  }
  hprdDataSorted$Samples.Int2<-count[j]
  }
}

1st Data.Frame looks as follows (csv):

HUGO.Int1,HUGO.Int2,barcode.Int1
A1CF,APOBEC1,TCGA-B6-A0RS-01A-11D-A099-09
A1CF,TNPO2,TCGA-B6-A0RS-01A-11D-A099-09
A1CF,SYNCRIP,TCGA-B6-A0RS-01A-11D-A099-09
A1CF,KHSRP,TCGA-B6-A0RS-01A-11D-A099-09
A2M,SHBG,TCGA-D8-A1JK-01A-11D-A13L-09
A2M,C11orf58,TCGA-D8-A1JK-01A-11D-A13L-09
A2M,ATF7IP,TCGA-D8-A1JK-01A-11D-A13L-09
AAMP,TH1L,TCGA-A8-A08S-01A-11W-A050-09
AARS,EEF1B2,TCGA-AO-A0JC-01A-11W-A071-09

2nd Data.frame which holds the duplicated barcodes (csv)

Sample_Barcode
TCGA-A8-A08G-01A-11W-A019-09
TCGA-AO-A03O-01A-11W-A019-09
TCGA-AO-A03O-01A-11W-A019-09
TCGA-B6-A0RS-01A-11D-A099-09
TCGA-BH-A0HP-01A-12D-A099-09
TCGA-BH-A0HP-01A-12D-A099-09
TCGA-BH-A18H-01A-11D-A12B-09
TCGA-BH-A18H-01A-11D-A12B-09
TCGA-BH-A18J-01A-11D-A12B-09
TCGA-D8-A1JK-01A-11D-A13L-09
TCGA-E2-A1BC-01A-11D-A14G-09
TCGA-E2-A1BC-01A-11D-A14G-09
TCGA-E9-A1NH-01A-11D-A14G-09
TCGA-E9-A22B-01A-11D-A159-09

If the barcode from barcode.Int1 (dataframe 1) is 3 times in Sample_barcode the script should add a 3 next to the barcode.Int1 the script is looking for. for example:

HUGO.Int1,HUGO.Int2,barcode.Int1, number_of_times
A1CF,APOBEC1,TCGA-B6-A0RS-01A-11D-A099-09,5

Answer 1

Paul’s comment is very appropriate, it will speed up the merge step significantly. I would use table to get the counts of the unique barcodes in your second data.frame and merge it onto your first, see below:

dat <- structure(list(HUGO.Int1 = c("A1CF", "A1CF", "A1CF", "A1CF", 
"A2M", "A2M", "A2M", "AAMP", "AARS"), HUGO.Int2 = c("APOBEC1", 
"TNPO2", "SYNCRIP", "KHSRP", "SHBG", "C11orf58", "ATF7IP", "TH1L", 
"EEF1B2"), barcode.Int1 = c("TCGA-B6-A0RS-01A-11D-A099-09", "TCGA-B6-A0RS-01A-11D-A099-09", 
"TCGA-B6-A0RS-01A-11D-A099-09", "TCGA-B6-A0RS-01A-11D-A099-09", 
"TCGA-D8-A1JK-01A-11D-A13L-09", "TCGA-D8-A1JK-01A-11D-A13L-09", 
"TCGA-D8-A1JK-01A-11D-A13L-09", "TCGA-A8-A08S-01A-11W-A050-09", 
"TCGA-AO-A0JC-01A-11W-A071-09")), .Names = c("HUGO.Int1", "HUGO.Int2", 
"barcode.Int1"), class = "data.frame", row.names = c(NA, -9L))

dat2 <- structure(list(Sample_Barcode = c("TCGA-A8-A08G-01A-11W-A019-09", 
"TCGA-AO-A03O-01A-11W-A019-09", "TCGA-AO-A03O-01A-11W-A019-09", 
"TCGA-B6-A0RS-01A-11D-A099-09", "TCGA-BH-A0HP-01A-12D-A099-09", 
"TCGA-BH-A0HP-01A-12D-A099-09", "TCGA-BH-A18H-01A-11D-A12B-09", 
"TCGA-BH-A18H-01A-11D-A12B-09", "TCGA-BH-A18J-01A-11D-A12B-09", 
"TCGA-D8-A1JK-01A-11D-A13L-09", "TCGA-E2-A1BC-01A-11D-A14G-09", 
"TCGA-E2-A1BC-01A-11D-A14G-09", "TCGA-E9-A1NH-01A-11D-A14G-09", 
"TCGA-E9-A22B-01A-11D-A159-09")), .Names = "Sample_Barcode", class = "data.frame", row.names = c(NA, 
-14L))

foo <- as.data.frame(table(dat2))
merge(dat, foo, by.x='barcode.Int1', by.y='dat2', all.x=TRUE)


#                   barcode.Int1 HUGO.Int1 HUGO.Int2 Freq
# 1 TCGA-A8-A08S-01A-11W-A050-09      AAMP      TH1L   NA
# 2 TCGA-AO-A0JC-01A-11W-A071-09      AARS    EEF1B2   NA
# 3 TCGA-B6-A0RS-01A-11D-A099-09      A1CF     TNPO2    1
# 4 TCGA-B6-A0RS-01A-11D-A099-09      A1CF   SYNCRIP    1
# 5 TCGA-B6-A0RS-01A-11D-A099-09      A1CF   APOBEC1    1
# 6 TCGA-B6-A0RS-01A-11D-A099-09      A1CF     KHSRP    1
# 7 TCGA-D8-A1JK-01A-11D-A13L-09       A2M  C11orf58    1
# 8 TCGA-D8-A1JK-01A-11D-A13L-09       A2M    ATF7IP    1
# 9 TCGA-D8-A1JK-01A-11D-A13L-09       A2M      SHBG    1

---

The data.table version:

library(data.table)

foo <- data.table(as.data.frame(table(dat2)))
setnames(foo, c('barcode.Int1', 'Freq'))
setkey(foo, barcode.Int1)

dat <- data.table(dat, key='barcode.Int1')

foo[dat]

#                    barcode.Int1 Freq HUGO.Int1 HUGO.Int2
# 1:                           NA   NA      AAMP      TH1L
# 2:                           NA   NA      AARS    EEF1B2
# 3: TCGA-B6-A0RS-01A-11D-A099-09    1      A1CF   APOBEC1
# 4: TCGA-B6-A0RS-01A-11D-A099-09    1      A1CF     TNPO2
# 5: TCGA-B6-A0RS-01A-11D-A099-09    1      A1CF   SYNCRIP
# 6: TCGA-B6-A0RS-01A-11D-A099-09    1      A1CF     KHSRP
# 7: TCGA-D8-A1JK-01A-11D-A13L-09    1       A2M      SHBG
# 8: TCGA-D8-A1JK-01A-11D-A13L-09    1       A2M  C11orf58
# 9: TCGA-D8-A1JK-01A-11D-A13L-09    1       A2M    ATF7IP

---

in “Pure” data.table:

dat <- data.table(dat, key='barcode.Int1')
dat2 <- data.table(dat2)
setnames(dat2, 'barcode.Int1')
setkey(dat2, barcode.Int1)

counts <- dat2[, list(count= .N), by=barcode.Int1]

counts[dat]