R读取数据出现“line 1 appears to contai
2019-04-20 本文已影响0人
浩瀚之宇
由于数据可能在Windows下编辑过，保存的是UTF-16的格式用R读取可能会出现以下问题。这种情况有以下三种解决方案。
> sampInfo=read.table("/media/xxx/sampInfo_origin.txt", na.strings=c("", "NA"), sep="\t", header=T)
Error in make.names(col.names, unique = TRUE) :
invalid multibyte string at '<ff><fe>R'
In addition: Warning messages:
1: In read.table("/media/xxx/sampInfo_origin.txt", :
line 1 appears to contain embedded nulls
2: In read.table("/media/xxx/sampInfo_origin.txt", :
line 2 appears to contain embedded nulls
3: In read.table("/media/xxx/sampInfo_origin.txt", :
line 3 appears to contain embedded nulls
4: In read.table("/media/xxx/sampInfo_origin.txt", :
line 4 appears to contain embedded nulls
5: In read.table("/media/albert/xxx/sampInfo_origin.txt", :
line 5 appears to contain embedded nulls
解决方法一：fileEncoding="UTF16LE"或者fileEncoding="UTF16"
> sampInfo=read.table("/media/xxx/sampInfo_origin.txt", fileEncoding="UTF16LE", sep="\t", header=T)
> sampInfo=read.table("/media/xxx/sampInfo_origin.txt", fileEncoding="UTF16", sep="\t", header=T)
> head(sampInfo)
Run Sample_Name age ancestry arthropathymeds biologics das_score
1 SRRxxx72 GSMxxx25 66 <NA> <NA> <NA> NA
2 SRRxxx73 GSMxxx26 72 <NA> <NA> <NA> NA
3 SRRxxx75 GSMxxx28 61 <NA> <NA> <NA> NA
4 SRRxxx74 GSMxxx27 72 <NA> <NA> <NA> NA
5 SRRxxx76 GSMxxx29 50 <NA> <NA> <NA> NA
6 SRRxxx77 GSMxxx30 59 <NA> <NA> <NA> NA
disease_activity donor gender leflumide nsaids othermeds phenotype
1 <NA> C137 male <NA> <NA> <NA> Healthy
2 <NA> C141 male <NA> <NA> <NA> Healthy
3 <NA> C383 male <NA> <NA> <NA> Healthy
4 <NA> C148 female <NA> <NA> <NA> Healthy
5 <NA> C391 female <NA> <NA> <NA> Healthy
6 <NA> C392 female <NA> <NA> <NA> Healthy
classification status plaquenil rituximab steroids sulfasalazine tissue
1 H H <NA> <NA> <NA> <NA> Blood
2 H H <NA> <NA> <NA> <NA> Blood
3 H H <NA> <NA> <NA> <NA> Blood
4 H H <NA> <NA> <NA> <NA> Blood
5 H H <NA> <NA> <NA> <NA> Blood
6 H H <NA> <NA> <NA> <NA> Blood
解决方法二：在Excel中打开，另存为csv文件即可。
> sampInfo=read.csv("/media/xxx/sampInfo_origin.csv", comment.char = "#", sep=",", header=T)
> head(sampInfo)
Run Sample_Name age ancestry arthropathymeds biologics das_score
1 SRRxxx72 GSMxxx25 66 <NA> <NA> <NA> NA
2 SRRxxx73 GSMxxx26 72 <NA> <NA> <NA> NA
3 SRRxxx75 GSMxxx28 61 <NA> <NA> <NA> NA
4 SRRxxx74 GSMxxx27 72 <NA> <NA> <NA> NA
5 SRRxxx76 GSMxxx29 50 <NA> <NA> <NA> NA
6 SRRxxx77 GSMxxx30 59 <NA> <NA> <NA> NA
disease_activity donor gender leflumide nsaids othermeds phenotype
1 <NA> C137 male <NA> <NA> <NA> Healthy
2 <NA> C141 male <NA> <NA> <NA> Healthy
3 <NA> C383 male <NA> <NA> <NA> Healthy
4 <NA> C148 female <NA> <NA> <NA> Healthy
5 <NA> C391 female <NA> <NA> <NA> Healthy
6 <NA> C392 female <NA> <NA> <NA> Healthy
classification status plaquenil rituximab steroids sulfasalazine tissue
1 H H <NA> <NA> <NA> <NA> Blood
2 H H <NA> <NA> <NA> <NA> Blood
3 H H <NA> <NA> <NA> <NA> Blood
4 H H <NA> <NA> <NA> <NA> Blood
5 H H <NA> <NA> <NA> <NA> Blood
6 H H <NA> <NA> <NA> <NA> Blood
解决方法三：在linux系统里将sampInfo_origin.txt用gedit打开，另存为sampInfo_origin01.txt，“Character Encoding” 改为 UTF-8， “Line ending”改为“Unix/Linux”。
> sampInfo=read.table("/media/xxx/sampInfo_origin01.txt", sep="\t", header=T)
> head(sampInfo,2)
Run Sample_Name age ancestry arthropathymeds biologics das_score
1 SRRxxx72 GSMxxx25 66 <NA> <NA> <NA> NA
2 SRRxxx73 GSMxxx26 72 <NA> <NA> <NA> NA
disease_activity donor gender leflumide nsaids othermeds phenotype
1 <NA> C137 male <NA> <NA> <NA> Healthy
2 <NA> C141 male <NA> <NA> <NA> Healthy
classification status plaquenil rituximab steroids sulfasalazine tissue
1 H H <NA> <NA> <NA> <NA> Blood
2 H H <NA> <NA> <NA> <NA> Blood
