[R] how do I remove entries in data frame from a vector

[Rui Barradas]

Hello,

This is probably because basename keeps the file extension, try instead


filename <- sub("(^[^\\.]*)\\..+$", "\\1", basename(celFiles))
celFiles[!filename %in% as.character(remove$V1)]


Hope this helps,

Rui Barradas

Às 22:15 de 21/10/20, Ana Marija escreveu:
> Hello,
> 
> I have a data frame with one column:
> 
>> remove
> 
>                                  V1
> 
> 1 ABAFT_g_4RWG569_BI_SNP_A10_35096
> 2 ABAFT_g_4RWG569_BI_SNP_B12_35130
> 3 ABAFT_g_4RWG569_BI_SNP_E09_35088
> 4 ABAFT_g_4RWG569_BI_SNP_E12_35136
> 5 ABAFT_g_4RWG569_BI_SNP_F11_35122
> 6 ABAFT_g_4RWG569_BI_SNP_F12_35138
> 7 ABAFT_g_4RWG569_BI_SNP_G07_35060
> 8 ABAFT_g_4RWG569_BI_SNP_G12_35140
> 
> I want to remove these 8 entries from remove data frame from this
> vector that looks like this:
> 
>> head(celFiles)
> 
> [1] "/GOKIND/75327/PhenoGenotypeFiles/RootStudyConsentSet_phs000018.GAIN_GoKinD.v2.p1.c1.DS-T1DCR-IRB/GenotypeFiles/ABAFT_g_4RWG569_BI_SNP_A01_34952.CEL"
> [2] "/GOKIND/75327/PhenoGenotypeFiles/RootStudyConsentSet_phs000018.GAIN_GoKinD.v2.p1.c1.DS-T1DCR-IRB/GenotypeFiles/ABAFT_g_4RWG569_BI_SNP_A02_34968.CEL"
> 
> [3] "/GOKIND/75327/PhenoGenotypeFiles/RootStudyConsentSet_phs000018.GAIN_GoKinD.v2.p1.c1.DS-T1DCR-IRB/GenotypeFiles/ABAFT_g_4RWG569_BI_SNP_A03_34984.CEL"
> 
> [4] "GOKIND/75327/PhenoGenotypeFiles/RootStudyConsentSet_phs000018.GAIN_GoKinD.v2.p1.c1.DS-T1DCR-IRB/GenotypeFiles/ABAFT_g_4RWG569_BI_SNP_A04_35000.CEL"
> 
> [5] "/GOKIND/75327/PhenoGenotypeFiles/RootStudyConsentSet_phs000018.GAIN_GoKinD.v2.p1.c1.DS-T1DCR-IRB/GenotypeFiles/ABAFT_g_4RWG569_BI_SNP_A05_35016.CEL"
> 
> [6] "/GOKIND/75327/PhenoGenotypeFiles/RootStudyConsentSet_phs000018.GAIN_GoKinD.v2.p1.c1.DS-T1DCR-IRB/GenotypeFiles/ABAFT_g_4RWG569_BI_SNP_A06_35032.CEL"
> ...
> 
> I tried doing this:
> 
> b= celFiles[!basename(celFiles) %in% as.character(remove$V1)]
> 
> but none of the 8th entries in "remove" data frame have been removed.
> 
> Please advise,
> Ana
> 
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