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Hello, I would like to try this example in this link: https://www.rdocumentation.org/packages/SNPRelate/versions/1.6.4/topics/snpgdsBED2GDS for example this line: bed.fn <- system.file("extdata", "plinkhapmap.bed.gz", package="SNPRelate") I have in...

Hi All, I have df like this: > df# A tibble: 2 ? 4 V1 n perc labels <chr> <int> <dbl> <chr> 1 Yes 8 0.364 36% 2 No 14 0.636 64% I am making pie chart like this: library...

Hi All, I have lines in file that look like this: > df[14509227,] SNP A1 A2 freq b se p N 1: <NA> <NA> <NA> NA NA NA NA NA data looks like this: > head(df) SNP A1 A2 freq...

Hello, I have a data frame like this: > head(b) FID IID FLASER PLASER 1: fam1000 G1000 1 1 2: fam1001 G1001 1 1 3: fam1003 G1003 1 2 4: fam1005 G1005 1 1 5: fam1009 G1009 2 1 6...

Hello, I have a dataframe (t1) with many columns, but the one I care about it this: > unique(t1$sex_chromosome_aneuploidy_f22019_0_0) [1] NA "Yes" it has these two values. I would like to remove from my...

Thanks, I did this: b$PHENO<- ifelse(b$FLASER ==2 | b$PLASER ==2, 2, 1) On Wed, Apr 29, 2020 at 2:36 PM Ivan Krylov <krylov.r00t at gmail.com> wrote: > > On Wed, 29 Apr 2020 14:19:18...

Hi Ivan Thanks for getting back to me. Can you please share with me some code I would use to see what is in my database? On Sat, 1 Feb 2020 at 06:19, Ivan Krylov <krylov.r00t at gmail...

Hi Bert, it gives me this: > a=load("paired_example.Rdata") > str(a) chr [1:3] "rawdata" "treatment" "patient" I don't know how to extract "treatment" for example in a data frame. I tried this but of no help...

Hi, I created a bar plot with this code: library(ggplot2) df <- data.frame("prop" = c(7.75,70.42), "Name" = c("All Genes","RG Genes")) p<-ggplot(data=df, aes(x=Name, y=prop,fill=Name)) + geom_bar(stat...

Hello, I am trying to use this program: https://github.com/kenhanscombe/ukbtools > my_ukb_data[1:3,1:3] eid sex_f31_0_0 year_of_birth_f34_0_0 1 1000017 Female 1938 2 1000025 Female 1951 3...

Hello, I have a data frame like this: > head(b) FID IID FLASER PLASER 1: fam1000 G1000 1 1 2: fam1001 G1001 1 1 3: fam1003 G1003 1 2 4: fam1005 G1005 1 1 5: fam1009 G1009 NA 2 6...

Thanks for getting back to me but I would need this text labels added in this particular instance On Wed, 11 Mar 2020 at 19:37, Abby Spurdle <spurdle.a at gmail.com> wrote: > > and I would like to get...

Hello, I am in process of writing a grant where I am explaining my planned methylation analysis using R software "minfi". In the text of the grant I am mentioning looking for samples containing outliers in the multi-dimensional scaling...

sorry not replace with NA but with empty string for a name, for example for example this: > geneSymbol["Ku8QhfS0n_hIOABXuE"] Ku8QhfS0n_hIOABXuE "MACC1" would go when I subject it to > geneSymbol["Ku8QhfS0n_hIOABXuE"] Ku8QhfS0n_hIOABXuE On Mon, Sep 14, 2020...

Hello, I got this error: Error: Cannot use `+.gg()` with a single argument. Did you accidentally put + on a new line? After running this: data(murders) library(ggplot2) library(dplyr) library(ggplot2) ggplot(data=murders) #define the slope of the...

Hello. I am trying to filter only rows that have ANY of these variables: E109, E119, E149 so I did: controls=t %>% filter_all(any_vars(. %in% c("E109", "E119","E149"))) than I checked what I got: > s0 <- sapply(controls...

I resolved it not elegantly with: d=as.numeric(as.character(e$pheno)) ed<-ggplot(e) + geom_bar(aes(x = ESRD, fill = factor(pheno,labels=c("control","case"))))+scale_fill_manual(values=c("#56B4E9","#E7B800"))+labs(fill="pheno")+scale_x...

Hello, I am making manhattan plot with: library(qqman) manhattan(a, chr="CHR", bp="BP", snp="SNP", p="P",annotatePval = 0.0001) and I would like to annotate these two SNPs which are above the threshold so that they have...

Hello, I tried your code and this is what I got I really need two groups side by side shown per chromosome as it is here: https://imgur.com/a/pj40c on the image there are 4 groups I do...

Hello, I do have a file like this: head M3.assoc.logistic.C CHR SNP BP P 1 1:785989:T:C 785989 0.4544 1 1:785989:T:C 785989 0.689 1 1:1130727:A:C 1130727 0...