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Ana Marija

2020-Oct-21 21:15 UTC

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

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

Rui Barradas

2020-Oct-21 21:41 UTC

head link

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

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

?s 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
> 
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

Rui Barradas

2020-Oct-21 21:47 UTC

head link

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

Hello,

To remove the file extension it's much easier to use base R


filename <- tools::file_path_sans_ext(basename(celFiles))


Hope this helps,

Rui Barradas

?s 22:41 de 21/10/20, Rui Barradas escreveu:> 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
> 
> ?s 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
>>
>> ______________________________________________
>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide 
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
> 
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide 
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

Rolf Turner

2020-Oct-21 22:46 UTC

head link

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

On Wed, 21 Oct 2020 16:15:22 -0500
Ana Marija <sokovic.anamarija at 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

Ana Marija

2020-Oct-21 23:27 UTC

head link

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

Makes sense, thank you!

On Wed, 21 Oct 2020 at 17:46, Rolf Turner <r.turner at auckland.ac.nz>
wrote:
>
> On Wed, 21 Oct 2020 16:15:22 -0500
> Ana Marija <sokovic.anamarija at 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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