沿着我的老问题Subsetting从DNAStringSet中定义了组,我很难对列表执行相同的操作。我所有导致错误的尝试:
Error in .Call2("new_XStringSet_from_CHARACTER", ans_class, ans_elementType, : key 56 (char '8') not in lookup table
工作示例: library("DECIPHER") library("Biostrings")
调用的DNAStringsets列表和调用Biglist
的选择项patterns
我想调用以获得新列表:
aDNAStringSet <- DNAStringSet(c("GCATCCATTAC", "AATCGCCATCC", "GCATACCTTAC", "GCATACCTTAC", "GCATACCTTAC"))
names(aDNAStringSet) <- c("seq1", "seq2", "seq3", "seq4", "seq5")
bDNAStringSet <- DNAStringSet(c("GCATCCATTAC", "AATCGCCATCC", "GCATACCTTAC", "GCATACCTTAC", "GCATACCTTAC"))
names(bDNAStringSet) <- c("seq1", "seq2", "seq3", "seq4", "seq5")
cDNAStringSet <- DNAStringSet(c("GCATCCATTAC", "AATCGCCATCC", "GCATACCTTAC", "GCATACCTTAC", "GCATACCTTAC"))
names(cDNAStringSet) <- c("seq1", "seq2", "seq3", "seq4", "seq5")
dDNAStringSet <- DNAStringSet(c("GCATCCATTAC", "AATCGCCATCC", "GCATACCTTAC", "GCATACCTTAC", "GCATACCTTAC"))
names(dDNAStringSet) <- c("seq1", "seq2", "seq3", "seq4", "seq5")
Biglist<-list(A=aDNAStringSet, B=bDNAStringSet, C=cDNAStringSet, D=dDNAStringSet)
patterns <- c("seq2", "seq4", "seq5")
使用Igrep
可以隔离elements
,但这不是我想要的:
newlist<-Biglist[grep("A", names(Biglist))]
使用lapply
应该是正确的方法,但是此行会导致错误:
newlist<-lapply(Biglist, function(y) y[y %in% patterns])
Error in .Call2("new_XStringSet_from_CHARACTER", ans_class, ans_elementType, : key 101 (char 'e') not in lookup table
我也听不懂错误讯息。有任何想法吗?
由于您正在使用S4类,因此,您需要一个不同的子集方法,在这种情况下, @
#To use `DNAStringSet` function install Biostrings using the following
#source("http://www.bioconductor.org/biocLite.R")
#biocLite(c("Biostrings"))
#library(Biostrings)
lapply(Biglist, function(x) x[x@ranges@NAMES %in% patterns])
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