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

[Ana Marija]

Makes sense, thank you!

On Wed, 21 Oct 2020 at 17:46, Rolf Turner <r.turner using auckland.ac.nz> wrote:

>
> On Wed, 21 Oct 2020 16:15:22 -0500
> Ana Marija <sokovic.anamarija using gmail.com> wrote:
>
> > 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$V1)]
> >
> > but none of the 8th entries in "remove" data frame have been removed.
> >
> > Please advise,
> > Ana
>
> I would advise you to *look* at basename(celFiles)!!!
>
> The entries end in ".CEL"; the names in remove$V1 do not.  So %in%
> finds no matches.  Perhaps:
>
>     b <- celFiles[!basename(celFiles) %in%
>                  paste0(as.character(remove$V1),".CEL")]
>
> Note that, for the data that you have presented, none of the entries of
> celFiles "match up" with "remove" so it is *still* the case that (for
> the data shown) none of the entries will be removed.  So your example
> was bad.
>
> cheers,
>
> Rolf Turner
>
> --
> Honorary Research Fellow
> Department of Statistics
> University of Auckland
> Phone: +64-9-373-7599 ext. 88276
>
>

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