Question

这很尴尬。我使用BSgenome编写DNAStringSet fasta文件，

writeXStringSet(DNAcutout1.seq, "DNAcutout1.fa", append=FALSE,
compress=FALSE,compression_level=NA, format="fasta")

但是当我运行另一个功能时，就说

library(NuPoP)
predNuPoP("DNAcutout1.fa", species=5, model=4)
[1] "The input file is not in FASTA format, or contains characters other than A/a,
C/c,G/g, T/t, N/n, stop!"

所以我想回去看看出了什么问题，但我不能使用read.DNAString

read.DNAStringSet(file="DNAcutout1.fa", format="fasta")
Error: could not find function "read.DNAStringSet"

请帮助！谢谢

> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets 
[7] methods   base     

other attached packages:
[1] NuPoP_1.14.1                          
[2] BSgenome.Dmelanogaster.UCSC.dm3_1.3.99
[3] BSgenome_1.32.0                       
[4] Biostrings_2.32.1                     
[5] XVector_0.4.0                         
[6] GenomicRanges_1.16.3                  
[7] GenomeInfoDb_1.0.2                    
[8] IRanges_1.22.10                       
[9] BiocGenerics_0.10.0                   
[10] BiocInstaller_1.14.2                  
[11] RSQLite_0.11.4                        
[12] DBI_0.2-7                             

loaded via a namespace (and not attached):
[1] bitops_1.0-6     Rsamtools_1.16.1 stats4_3.1.0    
[4] tools_3.1.0      zlibbioc_1.10.0

Answer 1

正如我在评论中提到的那样。 read.DNAStringSet已重命名为readDNAStringSet。请改用后一个函数名称

（在此发帖，因此问题不会显示为未答复）

错误：找不到函数＆＃34; read.DNAStringSet＆＃34;

1 个答案: