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