Dear Ana, pmax could also fit here. pmax(b$FLASER, b$PLASER, na.rm = TRUE)
Bests, Mark > ------------------------------ > > Message: 21 > Date: Sat, 13 Jun 2020 19:09:11 +1000 > From: Jim Lemon <drjimle...@gmail.com> > To: sokovic.anamar...@gmail.com > Cc: Rasmus Liland <j...@posteo.no>, r-help <r-help@r-project.org> > Subject: Re: [R] if else statement adjustemtn > Message-ID: > <ca+8x3fu6-wp1ct3ox6+iduvu7wl2m9thblbdsewub-8_vja...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Right, back from shopping. Since you have fourteen rows containing NAs > and you only want seven, we can infer that half of them must go. As > they are neatly divided into seven rows in which only one NA appears > and seven in which two stare meaninglessly out at us. I will assume > that the latter are the ones to be discarded. As your condition for > calculating "pheno" stated that a 2 in either FLASER or PLASER should > result in a 2 in pheno, the following statement closely conforms to > that: > > b<-read.table(text="FID IID FLASER PLASER > fam1837 G1837 1 NA > fam2410 G2410 NA NA > fam2838 G2838 NA 2 > fam3367 G3367 1 NA > fam3410 G3410 1 NA > fam3492 G3492 1 NA > fam0911 G911 NA NA > fam3834 G3834 2 NA > fam4708 G4708 NA 2 > fam5162 G5162 NA NA > fam5274 G5274 NA NA > fam0637 G637 NA NA > fam0640 G640 NA NA > fam0743 G743 NA NA > fam0911 G911 NA NA", > header=TRUE,stringsAsFactors=FALSE) > > b$pheno<-ifelse(b$FLASER == 2 | b$PLASER == 2,2,1) > # use the valid FLASER values when PLASER is NA > b[is.na(b$pheno),]$pheno<-ifelse(!is.na(b[is.na(b$pheno),]$FLASER), > b[is.na(b$pheno),]$FLASER,NA) > # use the valid PLASER values when FLASER if NA > b[is.na(b$pheno),]$pheno<-ifelse(!is.na(b[is.na(b$pheno),]$PLASER), > b[is.na(b$pheno),]$PLASER,NA) > b > > I could write that mess in one straitjacket of conditional statements > but my brain hurts enough. > > Jim > > > On Sat, Jun 13, 2020 at 1:59 PM Ana Marija <sokovic.anamar...@gmail.com> > wrote: > > > > Great idea! > > Here it is: > > > b[is.na(b$FLASER) | is.na(b$PLASER),] > > FID IID FLASER PLASER pheno > > 1: fam1837 G1837 1 NA 2 > > 2: fam2410 G2410 NA NA 2 > > 3: fam2838 G2838 NA 2 2 > > 4: fam3367 G3367 1 NA 2 > > 5: fam3410 G3410 1 NA 2 > > 6: fam3492 G3492 1 NA 2 > > 7: fam3834 G3834 2 NA 2 > > 8: fam4708 G4708 NA 2 2 > > 9: fam5162 G5162 NA NA 2 > > 10: fam5274 G5274 NA NA 2 > > 11: fam0637 G637 NA NA 2 > > 12: fam0640 G640 NA NA 2 > > 13: fam0743 G743 NA NA 2 > > 14: fam0911 G911 NA NA 2 > > > > On Fri, Jun 12, 2020 at 10:29 PM Jim Lemon <drjimle...@gmail.com> wrote: > > > > > > Since you have only a few troublesome NA values, if you look at them, > > > or even better, post them: > > > > > > b[is.na(b$FLASER) | is.na(b$PLASER),] > > > > > > perhaps we can work out the appropriate logic to get rid of only the > > > ones you don't want. > > > > > > Jim > > > > > > On Sat, Jun 13, 2020 at 12:50 PM Ana Marija <sokovic.anamar...@gmail.com> > > > wrote: > > > > > > > > Hi Rasmus, > > > > > > > > thank you for getting back to be, the command your provided seems to > > > > add all 11 NAs to 2s > > > > > b$pheno <- > > > > + ifelse(b$PLASER==2 | > > > > + b$FLASER==2 | > > > > + is.na(b$PLASER) | > > > > + is.na(b$PLASER) & b$FLASER %in% 1:2 | > > > > + is.na(b$FLASER) & b$PLASER == 2, > > > > + 2, 1) > > > > > table(b$pheno, exclude = NULL) > > > > > > > > 1 2 > > > > 859 839 > > > > > > > > Once again my desired results is to keep these 7 NAs as NAs > > > > > table(b$PLASER,b$FLASER, exclude = NULL) > > > > > > > > 1 2 3 <NA> > > > > 1 836 14 0 0 > > > > 2 691 70 43 2 > > > > 3 2 7 21 0 > > > > <NA> 4 1 0 7 > > > > > > > > and have > > > > 825 2s (825=691+14+70+7+43) > > > > and the rest would be 1s (866=1698-7-825) > > > > > > > > On Fri, Jun 12, 2020 at 9:29 PM Rasmus Liland <j...@posteo.no> wrote: > > > > > > > > > > On 2020-06-13 11:30 +1000, Jim Lemon wrote: > > > > > > On Fri, Jun 12, 2020 at 8:06 PM Jim Lemon wrote: > > > > > > > On Sat, Jun 13, 2020 at 10:46 AM Ana Marija wrote: > > > > > > > > > > > > > > > > I am trying to make a new column > > > > > > > > "pheno" so that I reduce the number > > > > > > > > of NAs > > > > > > > > > > > > > > it looks like those two NA values in > > > > > > > PLASER are the ones you want to drop. > > > > > > > > > > > > From just your summary table, it's hard to > > > > > > guess the distribution of NA values. > > > > > > > > > > Dear Ana, > > > > > > > > > > This small sample > > > > > > > > > > b <- read.table(text="FLASER;PLASER > > > > > 1;2 > > > > > ;2 > > > > > ; > > > > > 1; > > > > > 2; > > > > > 2;2 > > > > > 3;2 > > > > > 3;3 > > > > > 1;1", sep=";", header=TRUE) > > > > > > > > > > table(b$PLASER,b$FLASER, exclude = NULL) > > > > > > > > > > yields the same combinations you showed > > > > > earlier: > > > > > > > > > > 1 2 3 <NA> > > > > > 1 1 0 0 0 > > > > > 2 1 1 1 1 > > > > > 3 0 0 1 0 > > > > > <NA> 1 1 0 1 > > > > > > > > > > If you want to eliminate the four <NA>-based > > > > > combinations completely, this line > > > > > > > > > > b$pheno <- > > > > > ifelse(b$PLASER==2 | > > > > > b$FLASER==2 | > > > > > is.na(b$PLASER) | > > > > > is.na(b$PLASER) & b$FLASER %in% 1:2 | > > > > > is.na(b$FLASER) & b$PLASER == 2, > > > > > 2, 1) > > > > > table(b$pheno, exclude = NULL) > > > > > > > > > > will do it: > > > > > > > > > > 1 2 > > > > > 2 7 > > > > > > > > > > Best, > > > > > Rasmus > > > > > ______________________________________________ > > > > > R-help@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@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@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.
