我有一个非常慢的for循环并且无法正常工作，它在1个data.frame中查找条形码，而不是在另一个data.frame中搜索该条形码。第二个data.frame的bar_code可以有多次。每次找到条形码时，计数器都应计算条形码所在的次数，并将条形码数写入第1个数据框。
我的尝试：
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如下所示（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
第二个Data.frame，它包含重复的条形码（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
如果条形码.Int1（数据帧1）中的条形码在Sample_barcode中是3次，则脚本应在条形码旁边添加3，脚本正在寻找.Int1。例如：
HUGO.Int1,HUGO.Int2,barcode.Int1, number_of_times
A1CF,APOBEC1,TCGA-B6-A0RS-01A-11D-A099-09,5
答案 0 :(得分：5)
保罗的评论非常恰当，它将显着加快合并步骤。我会使用table来获取第二个data.frame中唯一条形码的计数，并merge将其计入您的第一个，见下文：
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
data.table版本：
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]