我有这个mystring分隔符_.这里的条件是如果有两个或多个分隔符,我想在第二个分隔符处拆分,如果只有一个分隔符,我想分割".Recal"并得到result如下所示的分隔符.

mystring<-c("MODY_60.2.ReCal.sort.bam","MODY_116.21_C4U.ReCal.sort.bam","MODY_116.3_C2RX-1-10.ReCal.sort.bam","MODY_116.4.ReCal.sort.bam")

结果

"MODY_60.2"  "MODY_116.21" "MODY_116.3"  "MODY_116.4"

我有这个数据帧mydf.该列nucleotide可以有'A','T','G','C'字母.如果A列是' - ' ,我想将字母A更改为T,C更改为G,G更改为C,将T更改为A. 我该怎么做？

  mydf<- structure(list(seqnames = structure(c(1L, 1L, 1L, 1L), .Label = c("chr1", 
    "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", 
    "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", 
    "chr17", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", 
    "chrY", "chrM"), class = "factor"), pos = c(115258748, 115258748, 
    115258748, 115258748), strand = structure(c(1L, 2L, 1L, 2L), .Label = c("+", 
    "-", "*"), class = "factor"), nucleotide = structure(c(2L, 2L, 
    2L, 2L), .Label = c("A", "C", "G", "T", …

我有一个名为 的数据框tt。我想创建一个名为 Ethnicity 的新列，其中我希望为超过 80% 的每一行值设置一个列标题。如果没有行具有大于 80% 的值，那么我希望该行中有字符串“MIX”。

tt <- structure(list(INDIVIDUAL = c("SJL0253301", "SJL1073801", "SJL1066401", 
"SJL1762813"), EUR = c(0.974378, 0.496489, 1e-05, 1e-05), EAS = c(0.010592, 
0.438799, 0.99996, 1e-05), AMR = c(0.004699, 1e-05, 1e-05, 0.99996
), SAS = c(1e-05, 0.053618, 1e-05, 1e-05), AFR = c(0.010321, 
0.011084, 1e-05, 1e-05)), row.names = c(1L, 44L, 19L, 911L), class = "data.frame")

我想要的结果：

INDIVIDUAL      EUR      EAS      AMR      SAS      AFR Ethnicity
SJL0253301 0.974378 0.010592 0.004699 0.000010 0.010321 EUR
SJL1073801 0.496489 0.438799 0.000010 0.053618 0.011084 MIX …

我试图RMySQL通过R studio 安装在Ubuntu中,但我遇到了下面的错误.请有人帮我解决这个问题.

Installing package into ‘/R_latest/lib/R/library’
(as ‘lib’ is unspecified)
--2015-11-18 11:40:26--  https://cran.rstudio.com/src/contrib/RMySQL_0.10.7.tar.gz
Resolving cran.rstudio.com (cran.rstudio.com)... 54.230.132.47
Connecting to cran.rstudio.com (cran.rstudio.com)|54.230.132.47|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 52422 (51K) [application/x-gzip]
Saving to: '/tmp/Rtmp52166B/downloaded_packages/RMySQL_0.10.7.tar.gz’

     0K .......... .......... .......... .......... .......... 97% 1.73M 0s
    50K .                                                     100% 2276G=0.03s

2015-11-18 11:40:26 (1.77 MB/s) - '/tmp/Rtmp52166B/downloaded_packages/RMySQL_0.10.7.tar.gz’ saved [52422/52422]

* installing *source* package ‘RMySQL’ ...
** package ‘RMySQL’ successfully unpacked and MD5 sums checked
Using PKG_CFLAGS=
Using PKG_LIBS=-lmysqlclient -lz …

我的变量名称格式如下：

PP_Sample_12.GT

或者

PP_Sample-17.GT

我正在尝试使用字符串拆分来 grep 出中间部分： ieSample_12或Sample-17. 但是，当我这样做时：

IDtmp <- sapply(strsplit(names(df[c(1:13)]),'_'),function(x) x[2])
IDs <- data.frame(sapply(strsplit(IDtmp,'.GT',fixed=T),function(x) x[1]))

我最终得到的Sample是PP_Sample_12.GT。

还有其他方法可以做到这一点吗？也许使用模式/替换类型的函数？不过，不确定 R 中是否存在（但我认为这可能适用gsub）

我有一个叫做的矩阵mymat.我有一个叫做的矢量geno <- c("01","N1","11","1N","10").我有另一张桌子叫key.table.我想要做的是我想匹配key列中key.table的key列mymat和如果任何匹配行中的列值具有任何geno元素,我想从mymat匹配geno元素中提取该列名称并粘贴它在新列matched.extract中key.table为每个相应的行key并得到结果.

  mymat <- structure(c("chr5:12111", "chr5:12111", "chr5:12113", "chr5:12114", 
"chr5:12118", "0N", "0N", "1N", "0N", "0N", "00", "00", "00", 
"11", "10", "00", "00", "1N", "0N", "00"), .Dim = c(5L, 4L), .Dimnames = list(
    c("34", "35", "36", "37", "38"), c("key", "AMLM12001KP", 
    "AMAS-11.3-Diagnostic", "AMLM12014N-R")))

key.table<- structure(c("chr5:12111", "chr5:12111", "chr5:12113", "chr5:12114", 
"chr5:12118", "chr5:12122", "chr5:12123", "chr5:12123", "chr5:12125", 
"chr5:12127", "chr5:12129", "9920068", …

我有一个dd2包含数百列的数据框,我需要做的是将所有这些列值粘贴在一起,省略任何NA值.如果我做这样的事情

apply(dd2, 1, paste, collapse=",")

它实际上包括NAs作为"NA"字符串.我想避免这种情况.我也可以如下所示,但是这会让我一次为每个单独的列工作以获得结果.

result <- cbind(    
    dd2, 
    combination = paste(dd2[,2], replace(dd2[,3], is.na(dd2[,3]), ""), sep = ",")
)

有没有有效的方法呢？以下是示例数据:

dd2 <- structure(c("A", "B", "C", "D", "E", "AK2", "HFM1", NA, "TRR", 
"RTT", NA, "PPT", "TRR", "RTT", NA, "PPT", NA, NA, "GGT", NA), .Dim = c(5L, 
4L), .Dimnames = list(NULL, c("sample_id", "plant", "animal", 
"more")))

我需要在 R 中读取至少 10 GB 大小的文件。为了限制内存使用，我只想读取那些匹配模式的行。例如，在mytext.tsv下面的文本文件中，我想从将成为标题的想要的行中读取。然后读取匹配coding和synonymousfrom的行col2，即patterns。

patterns <- c("coding", "synonymous")

mytext.tsv：

## lines unwanted
## lines unwanted1
## lines unwanted2
## lines unwanted3
wanted  col1       col2    
aaa     variant1   coding
jhjh    variant2   non-coding
ggg     variant3   synonymous
fgg     variant4   coding
gdg     variant6   missense  

我预期的数据框应该是：

wanted  col1       col2    
aaa     variant1   coding
ggg     variant3   synonymous

我知道我可以使用连接和扫描然后循环遍历每个模式，但是在 R 中有什么有效的方法可以做到这一点吗？

我的实际数据示例：

我需要帮助合并数据（mydf）中具有相同名称（即起始列）的行，并连接“ALT”列中的内容，从而根据起始列中的相似值删除所有重复行。我想合并行并连接“ALT”列中用逗号分隔的内容，并得到如下所示的结果。感谢您的帮助。

> mydf
         chr          start      end REF ALT         TYPE refGene               
       chr10 chr10:176131 176131   C   A          snp nonsynonymous SNV 
       chr10 chr10:159149 159149   C   G snp:17659149 nonsynonymous SNV 
       chr10 chr10:159149 159149   C   T snp:17659149 nonsynonymous SNV 
       chr10 chr10:241469 241469   T   C          snp          splicing 

> result
         chr          start      end REF ALT         TYPE refGene                   
       chr10 chr10:176131 176131   C   A          snp nonsynonymous SNV 
       chr10 chr10:159149 159149   C   G,T snp:17659149 nonsynonymous SNV 
       chr10 chr10:241469 241469   T   C          snp          splicing 

DPUT 在这里：

structure(list(chr = c("chr3", "chr3", "chr3", …

我有一个数据框,mydf其中n列具有相同的列名称name.我想将它们更改为name1 name2 and name3 ..name-nth列.我如何在R中做到这一点？