如何使用高级字符串匹配对数据进行子集化 [英] How to subset data with advance string matching
问题描述
我有以下数据框,我想根据匹配的字符串从中提取行.
I have the following data frame from which I would like to extract rows based on matching strings.
> GEMA_EO5
gene_symbol fold_EO p_value RefSeq_ID BH_p_value
KNG1 3.433049 8.56e-28 NM_000893,NM_001102416 1.234245e-24
REXO4 3.245317 1.78e-27 NM_020385 2.281367e-24
VPS29 3.827665 2.22e-25 NM_057180,NM_016226 2.560770e-22
CYP51A1 3.363149 5.95e-25 NM_000786,NM_001146152 6.239386e-22
TNPO2 4.707600 1.60e-23 NM_001136195,NM_001136196,NM_013433 1.538000e-20
NSDHL 2.703922 6.74e-23 NM_001129765,NM_015922 5.980454e-20
DPYSL2 5.097382 1.29e-22 NM_001386 1.062868e-19
所以我想提取例如基于 $RefSeq_ID 中匹配字符串的两行,适用于以下内容:
So I would like to extract e.g. two rows based on matching strings in $RefSeq_ID, that works fine with the following:
> list<-c("NM_001386", "NM_020385")
> GEMA_EO6<-subset(GEMA_EO5, GEMA_EO5$RefSeq_ID %in% list, drop = TRUE)
> GEMA_EO6
gene_symbol fold_EO p_value RefSeq_ID BH_p_value
REXO4 3.245317 1.78e-27 NM_020385 2.281367e-24
DPYSL2 5.097382 1.29e-22 NM_001386 1.062868e-19
但有些行有几个用逗号分隔的 RefSeq_ID,所以我正在寻找一种通用方法来判断 $RefSeq_ID 是否包含某个字符串模式,然后对该行进行子集化.
But some of the rows have several RefSeq_IDs separated with commas, so I am looking for a general way of telling if $RefSeq_ID contains a certain string pattern and then subset that row.
推荐答案
要进行部分匹配,您需要使用正则表达式(请参阅 ?grepl
).这是您的特定问题的解决方案:
To do partial matching you'll need to use regular expressions (see ?grepl
). Here's a solution to your particular problem:
##Notice that the first element appears in
##a row containing commas
l = c( "NM_013433", "NM_001386", "NM_020385")
要一次测试一个序列,我们只需选择一个特定的 seq id:
To test one sequence at a time, we just select a particular seq id:
R> subset(GEMA_EO5, grepl(l[1], GEMA_EO5$RefSeq_ID))
gene_symbol fold_EO p_value RefSeq_ID BH_p_value
5 TNPO2 4.708 1.6e-23 NM_001136195,NM_001136196,NM_013433 1.538e-20
为了检测多个基因,我们使用 |
操作符:
To test for multiple genes, we use the |
operator:
R> paste(l, collapse="|")
[1] "NM_013433|NM_001386|NM_020385"
R> grepl(paste(l, collapse="|"),GEMA_EO5$RefSeq_ID)
[1] FALSE TRUE FALSE FALSE TRUE FALSE TRUE
所以
subset(GEMA_EO5, grepl(paste(l, collapse="|"),GEMA_EO5$RefSeq_ID))
应该给你你想要的.
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