Search Archives
Search tips
from:Name
Search by author name, e.g. from:Duncan Murdoch
"exact phrase"
Match an exact phrase
word1 word2
Match messages containing both words
Date range
Use the date pickers to filter results to a time period
Use the list dropdown to narrow results to a specific mailing list. Combine from: with other terms to filter by author and content.
Hello, I have my normalized data matrix in file:normalizedDataMatrix_filtered.RData how do I have that in .csv format? Thanks Ana
Hello, Can I apply the quantile function qt() this way? qt(pvals/2, 406-34, lower.tail = F) to get the T-scores? Thanks Ama
Hello, I have a database DGN-WB_0.5.db is there is a way to explore its content in R? I don't know anything about this data base. Thanks Ana
Hello, I have this file: > a=load("paired_example.Rdata") > a [1] "rawdata" "treatment" "patient" I can extract "rawdata" with: dat<-local(get(load("paired_example.Rdata"))) Can you please advise how would I extract in data frame "treatment" and...
Hello, I tried doing: > library(vcfR) > vcf <- read.vcfR("ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf", verbose = FALSE ) but this takes forever to load and I am not sure it is even working. Any other suggestion on...
Hello, I have a set of two conditions: individual.variance and intra.individual.variance with their p values. Does it make sense to compare variances between those two groups with F test via: var.test(b$inter.individual.variance, b...
Hello, Hello, I have a data frame (tot) with about 2000 columns. How can I extract from it all strings that start with E14? I tried this: e14 <- sapply(tot, function(x) grepl("^E14", x)) but this returns me just...
Hello, I made plot in attach using: boxplot(flcn_M~subject,data=dx,col = c("royalblue1","palevioletred1"),xlab="subjects",ylab="Expression estimate in delta (log2)",boxwex = 0.2,frame.plot = FALSE) stripchart(flcn_M~subject, vertical = TRUE, data = dx,method...
Hello, Is there is a way to set colors in this plot to look like this one in attach (different color for each CHR-there is 22 of them)? library(qqman) results_log <- read.table("meta_p_pos_chr.F...
Hello, I have a vector like this: > head(geneSymbol) Ku8QhfS0n_hIOABXuE Bx496XsFXiAlj.Eaeo W38p0ogk.wIBVRXllY QIBkqIS9LR5DfTlTS8 BZKiEvS0eQ305U0v34 6TheVd.HiE1UF3lX6g "MACC1" "GGACT" "A4GALT" "NPSR1-AS1" "NPSR1-AS1" "AAAS" it has around 15000 entries. How do I replace all values with NA...
Hello, I have a data frame: > dim(tot) [1] 502536 1093 How would I extract from it all strings that start with E10? I know how to extract all rows that contain with E10 df0<-tot %>% filter_all(any_vars...
Hello, I have a data frame tot which has many columns and many rows. I am trying to find all columns that have say a value in any of their rows that STARTS WITH: "E94" for example there are columns...
Hello, I am trying to run this code: https://github.com/eleporcu/TWMR/blob/master/MR.R with r-3.6.1 via: Rscript MR.R --no-save ENSG00000154803 in the current directory I have saved: ENSG00000154803.ld and ENSG00000154803...
Hello, I have a dataframe like this: Chr BP Marker MAF A1 A2 Direction pValue N 1 10 100000625 10:100000625:A:G 0.416562 G A - 0.558228 1594 2 10 100000645 10:100000645:A:C 0.215182 C...
Hello, I would like to calculate a p value from two distributions, one looks like this: > head(b) gene_id number_of_eqtles_per_gene 1: ENSG00000237683.5 5 2: ENSG00000225972.1 267 3: ENSG00000225630.1 97 4: ENSG00000237973.1...
Hi, I was using this library, qqman https://cran.r-project.org/web/packages/qqman/vignettes/qqman.html to create QQ plot, attached. How would I change this default abline to start from the beginning of my QQ line? This...
Hello, I made the plot in attach via: 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") ed How do I show only 1...
Hello, I am filtering my data frame "tot" via: controls=tot %>% filter_all(any_vars(. %in% c("E109", "E119","E149"))) %>% filter_all(any_vars(. %in% c("Caucasian"))) %>% filter_all(any_vars(. %in% c("No kinship found","Ten or more third...
Hi, I have a data frame like this: > head(a) FID LASER2 CURRELIG PLASER RTNPTHY 1 fam1000_G1000 1 1 1 1 2 fam1001_G1001 1 1 1 1 3 fam1003_G1003 2 1 2 2 4 fam1005_G1005 1...
Hello, I tried using qvalue function: library(qvalue) qval_obj=qvalue(pvalR) pi1=1-qval_obj$pi0 but after running: qval_obj=qvalue(pvalR) Error in smooth.spline(lambda, pi0, df = smooth.df) : missing or infinite values in inputs are...
Can't find what you're looking for? Try searching with Google .