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