如何基于R的部分字符串匹配合并两个数据帧? [英] How to merge two data frame based on partial string match with R?
问题描述
我有两个数据框:
第一个包含大量的蛋白质，我对此进行了多次计算.这里是一个例子:
the first one contains a huge number of proteins for which I have made several calculations. here an example:
>Accession Description # Peptides A2 # PSM A2 # Peptides B2 # PSM B2 # Peptides C2 # PSM C2 # Peptides D2 # PSM D2 # Peptides E2 # PSM E2 # AAs MW [kDa] calc. pI
P01837 Ig kappa chain C region OS=Mus musculus PE=1 SV=1 - [IGKC_MOUSE] 10 319 8 128 8 116 7 114 106 11,8 5,41
P01868 Ig gamma-1 chain C region secreted form OS=Mus musculus GN=Ighg1 PE=1 SV=1 - [IGHG1_MOUSE] 13 251 15 122 16 116 16 108 324 35,7 7,40
P60710 Actin, cytoplasmic 1 OS=Mus musculus GN=Actb PE=1 SV=1 - [ACTB_MOUSE] 15 215 10 37 11 30 11 31 16 154 375 41,7 5,48
第二个包含目的蛋白.这里是一个例子:
the second contains the proteins of interest. here an example:
>complex Description Accession protein
TFIID [TAF1_MOUSE] Q80UV9-3 Isoform 3 of Transcription initiation factor TFIID subunit 1 OS=Mus musculus GN=Taf1 - [TAF1_MOUSE]
TFIID [TAF2_MOUSE] Q8C176 Transcription initiation factor TFIID subunit 2 OS=Mus musculus GN=Taf2 PE=2 SV=2 - [TAF2_MOUSE]
TFIID [TAF3_MOUSE] Q5HZG4 Transcription initiation factor TFIID subunit 3 OS=Mus musculus GN=Taf3 PE=1 SV=2 - [TAF3_MOUSE]
我想做的:从我的计算中得到一个仅包含目标蛋白质值的数据框.在第一次尝试中，我使用了:
What I want to do: get one data frame containing the values from my calculations for the proteins of interest only. In a first attempt I used:
fusion <- merge.data.frame(x=tableaucleanIPTAFXwoNA, y=sublist, by.x="Description", by.y="protein", all =FALSE)
但是，两个数据框之间蛋白质名称的命名方式是不同的，并且使用合并功能无法正常工作.
However, the nomenclature of the protein names are different between the two data frames and using the merge function this does not work.
那么，当"TAF10"是转录起始因子TFIID亚基10 OS =小家鼠GN = Taf10 PE = 1 SV = 1-[TAF10_MOUSE]"字符串文本的一部分时，我该如何部分匹配? 换句话说，我希望R只能识别整个字符串中的一部分.
So, how could I perform a partial match for "TAF10" when it is part of "Transcription initiation factor TFIID subunit 10 OS=Mus musculus GN=Taf10 PE=1 SV=1 - [TAF10_MOUSE]" string text ? In other words I want R recognizes only a piece o f the whole string.
我尝试使用grep函数:
I tried to use grep function:
idx2 <- sapply("tableaucleanIPTAFX$Description", grep, "sublist$Description")
但是，我明白了:
as.data.frame(idx2)
[1] tableaucleanIPTAFX.Description
<0 rows> (or 0-length row.names)
我猜想，该模式未被正确识别...然后，我访问了RegExr网站以编写一个正则表达式，以便可以识别我的ID名称.我发现这样做可以将[TRRAP_MOUSE]识别为
I guess that, the pattern is not correctly recognized... Then I visited the RegExr website to write a regular expression so that my id names can be recognized. I found that this works to recognize [TRRAP_MOUSE] into
与转化/转录域相关的蛋白OS =小家鼠GN =陷阱PE = 1 SV = 2-[TRRAP_MOUSE] :
Transformation/transcription domain-associated protein OS=Mus musculus GN=Trrap PE=1 SV=2 - [TRRAP_MOUSE] :
使用
/(TRRAP_[MOUSE])\w+/g
我想知道如何将其实现到我的ID列表(示例中的"Description"列)吗?
I wonder how I can implement it to my id list (the "Description" column in my example) ?
推荐答案
这可能对您有用，并且可以处理重复项:
This might work for you and it handles duplicates:
首先是一些伪数据:
df1 <- data.frame(name=c("George", "Abraham", "Barack"), stringsAsFactors = F)
df2 <- data.frame(president=c("Thanks, Obama (Barack)","Lincoln, Abraham, George""George Washington"), stringsAsFactors = F)
使用grep查找完整描述中的代码:
Find the code in the full description using grep:
idx2 <- sapply(df1$name, grep, df2$president)
如果多个描述与代码匹配，则可能导致多个匹配，因此在这里我重复原始索引，以便结果对齐:
This can result in multiple matches if multiple descriptions match the code so here I duplicate the original indices so the results align:
idx1 <- sapply(seq_along(idx2), function(i) rep(i, length(idx2[[i]])))
合并" cbind与新索引对齐的数据集:
"merge" the datasets with cbind aligned on the new indices:
> cbind(df1[unlist(idx1),,drop=F], df2[unlist(idx2),,drop=F])
name president
1 George Lincoln, Abraham, George
1.1 George George Washington
2 Abraham Lincoln, Abraham, George
3 Barack Thanks, Obama (Barack)
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