search for: queryhits

...n to newer version. That time I have also updated the RStudio software. After that when I have tried to install the package named "methyAnalysis". It shows some error given below. No methods found in package ?IRanges? for requests: ?%in%?, ?elementLengths?, ?elementMetadata?, ?ifelse?, ?queryHits?, ?Rle?, ?subjectHits?, ?t? when loading ?bumphunter? Error: package or namespace load failed for ?methyAnalysis?: objects ?.__T__split:base?, ?split? are not exported by 'namespace:IRanges' In addition: Warning message: replacing previous import ?BiocGenerics::image? by ?graphics::image?...

...e RStudio software. >> >> After that when I have tried to install the package named "methyAnalysis". >> It shows some error given below. >> >> No methods found in package ?IRanges? for requests: ?%in%?, >> ?elementLengths?, ?elementMetadata?, ?ifelse?, ?queryHits?, ?Rle?, >> ?subjectHits?, ?t? when loading ?bumphunter? >> Error: package or namespace load failed for ?methyAnalysis?: >> objects ?.__T__split:base?, ?split? are not exported by >> 'namespace:IRanges' >> In addition: Warning message: >> replacing prev...

Hi, I want to merge multiple chromosomal regions based on their common intersecting regions. I tried couple of things using while and if loops but did not work out. I would appreciate if anyone could provide me a small piece of code in R to get the intersection of following example: chr1: 100-150 chr1: 79-250 chr1: 100-175 chr1: 300-350 I want the intersection of all four regions as follow:

...I have also updated the RStudio software. > > After that when I have tried to install the package named "methyAnalysis". > It shows some error given below. > > No methods found in package ?IRanges? for requests: ?%in%?, > ?elementLengths?, ?elementMetadata?, ?ifelse?, ?queryHits?, ?Rle?, > ?subjectHits?, ?t? when loading ?bumphunter? > Error: package or namespace load failed for ?methyAnalysis?: > objects ?.__T__split:base?, ?split? are not exported by 'namespace:IRanges' > In addition: Warning message: > replacing previous import ?BiocGenerics::im...

Hi All, I have an CBS segmentation algorithm output for 10 tumor samples each from 2 different tumors. Now, I am in an urgent need to assign gene (followed by all genes present) that belong to a particular segment after I removed all the CNVs from segment data. The format of the data is: Sample Chromosome Start End Num_Probes Segment_Mean Sample1A-TA 1 51598 76187 15

..., ranges = IRanges(start = mp[[1]], end = mp[[1]]+(mp[,2]-1)), strand = rep("+", nrow(mp))) #OL <- findOverlaps(query=gr, subject=annotGr) OL.p <- annotGr[(!is.na(match(annotGr, gr)))] #as.data.frame(OL) ## view the results #tdata.p <- annotGr[unique(queryHits(OL)),] #tdata.p <- as.data.frame(tdata.p, row.names = NULL, optional = FALSE) #write.table(tdata.p, paste(i,"plus.txt")) cat( paste(i,"plus.txt\n")) } OL.m <- NULL if(nrow(mm) > 0) { ##### MATCH THE MINUS STRAND ######## #need to ge...

Hi everybody, I would like to know whether it is possible to compare to tables for certain parameters. I have these two tables: gene table name chr start end str accession Length gen1 4 646752 646838 + MI0005806 86 gen12 2L 243035 243141 - MI0005821 106 gen3 2L 159838 159928 + MI0005813 90 gen7 2L

Hello, I'm trying to use coxph() function to fit a very simple Cox proportional hazards regression model (only one covariate) but the parameter space is restricted to an open set (0, 1). Can I still obtain a valid estimate by using coxph function in this scenario? If yes, how? Any suggestion would be greatly appreciated. Thanks!!! [[alternative HTML version deleted]]