我试图找到一种优雅的方法来查找数据框中两个字符列之间的匹配。复杂的部分是，任何一个字符串都可以包含一个逗号分隔的列表，如果一个列表的成员与另一个列表的任何成员匹配，那么整个条目都将被视为匹配。我不确定我解释得有多好，所以这里是示例数据和输出：
备选1：

• AT
• A
• G
• CGTCC、AT
• CGC

Alt2：

• AA
• A
• GG
• AT、GGT
• 共格

每行的预期匹配：

• 第1行=无
• 第2行= A
• 第3行=无
• 第4行= AT
• 第5行=无

非工作溶液：
首次尝试：按所需列合并整个数据框，然后匹配上面显示的alt列：

match1 = data.frame(merge(vcf.df, ref.df, by=c("chr", "start", "end",  "ref")))
matches = unique(match1[unlist(sapply(match1$Alt1 grep, match1$Alt2, fixed=TRUE)),])

第二种方法，使用来自VariantAnnoatation/Granges的findoverlaps特征：

findoverlaps(ranges(vcf1), ranges(vcf2))

任何建议将不胜感激！谢谢！

解决方案感谢@马拉特Talipov在下面的回答，下面的解决方案可以比较两个逗号分隔的字符串：

> ##read in edited kaviar vcf and human ref
> ref <-     readVcfAsVRanges("ref.vcf.gz", humie_ref)
Warning message:
In .vcf_usertag(map, tag, ...) :
  ScanVcfParam ‘geno’ fields not present: ‘AD’

> ##rename chromosomes to match with vcf files
> ref <- renameSeqlevels(ref, c("1"="chr1"))

> ##################################
> ## Gather VCF files to process  ## 
> ##################################
> ##data frame *.vcf.gz files in directory path
> vcf_path <- data.frame(path=list.files(vcf_dir, pattern="*.vcf.gz$",  full=TRUE))

> ##read in everything but sample data for speediness
> vcf_param = ScanVcfParam(samples=NA)
> vcf <- readVcfAsVRanges("test.vcf.gz", humie_ref, param=vcf_param)

> #################
> ## Match SNP's ##
> #################
> ##create data frames of info to match on
> vcf.df = data.frame(chr =as.character(seqnames(vcf)), start = start(vcf),     end = end(vcf), ref = as.character(ref(vcf)), 
+                     alt=alt(vcf), stringsAsFactors=FALSE)
> ref.df = data.frame(chr =as.character(seqnames(ref)), start =     start(ref), end = end(ref), 
+                     ref = as.character(ref(ref)), alt=alt(ref),     stringsAsFactors=FALSE)
> 
> ##merge based on all positional fields except vcf
> col_match = data.frame(merge(vcf.df, ref.df, by=c("chr", "start", "end", "ref")))

> library(stringi)
> ##split each alt column by comma and bind together
> M1 <- stri_list2matrix(sapply(col_match$alt.x,strsplit,','))
> M2 <- stri_list2matrix(sapply(col_match$alt.y,strsplit,','))
> M <- rbind(M1,M2)

> ##compare results
> result <- apply(M,2,function(z) unique(na.omit(z[duplicated(z)])))

> ##add results column to col_match df for checking/subsetting
> col_match$match = result
> head(col_match)
   chr    start      end ref alt.x alt.y match
1 chr1 39998059 39998059   A     G     G     G
2 chr1 39998059 39998059   A     G     G     G
3 chr1 39998084 39998084   C     A     A     A
4 chr1 39998084 39998084   C     A     A     A
5 chr1 39998085 39998085   G     A     A     A
6 chr1 39998085 39998085   G     A     A     A