bioconductor

问题 I want to retrieve the genes that are present within a series of regions. Say, I have a bed file with query positions such like: 1 2665697 4665777 MIR201 1 10391435 12391516 MIR500 1 15106831 17106911 MIR122 1 23436535 25436616 MIR234 1 23436575 25436656 MIR488 I would like to get the genes that fall within those regions. I have tried using biomaRt , and bedtools intersect, but the output I get, is a list of genes corresponding to all the regions, not one by one, as the desired output I would

问题 I'm loading a built-in ideogram from the biovizBase package: data("hg19Ideogram", package = "biovizBase") The actual object is fine when inspected with str : > hg19Ideogram %>% str Formal class 'GRanges' [package "GenomicRanges"] with 6 slots ..@ seqnames :Formal class 'Rle' [package "IRanges"] with 4 slots .. .. ..@ values : Factor w/ 93 levels "chr1","chr1_gl000191_random",..: 1 2 3 4 5 6 7 8 9 10 ... .. .. ..@ lengths : int [1:93] 1 1 1 1 1 1 1 1 1 1 ... .. .. ..@ elementMetadata: NULL ..

问题 I'm loading a built-in ideogram from the biovizBase package: data("hg19Ideogram", package = "biovizBase") The actual object is fine when inspected with str : > hg19Ideogram %>% str Formal class 'GRanges' [package "GenomicRanges"] with 6 slots ..@ seqnames :Formal class 'Rle' [package "IRanges"] with 4 slots .. .. ..@ values : Factor w/ 93 levels "chr1","chr1_gl000191_random",..: 1 2 3 4 5 6 7 8 9 10 ... .. .. ..@ lengths : int [1:93] 1 1 1 1 1 1 1 1 1 1 ... .. .. ..@ elementMetadata: NULL ..

问题 I'm replacing gregexpr with gregexpr2 to detect overlapping matches. When I try. >subSeq 3000-letter "DNAString" instance seq: ACACGTGTTCTATTTTCATTTGCTGACATTTTCTAGTGCATCATTTTTTATTTTATTTTCATT.... gregexpr2("TAAT|ATTA",subSeq) Error in matches[[i]] : subscript out of bounds whereas gregexpr("TAAT|ATTA",subSeq) works fine. What happened? 回答1: It is quite clear if you read gregexpr2 documentation: This is a replacement for the standard gregexpr function that does exact matching only. Standard

问题 I'm replacing gregexpr with gregexpr2 to detect overlapping matches. When I try. >subSeq 3000-letter "DNAString" instance seq: ACACGTGTTCTATTTTCATTTGCTGACATTTTCTAGTGCATCATTTTTTATTTTATTTTCATT.... gregexpr2("TAAT|ATTA",subSeq) Error in matches[[i]] : subscript out of bounds whereas gregexpr("TAAT|ATTA",subSeq) works fine. What happened? 回答1: It is quite clear if you read gregexpr2 documentation: This is a replacement for the standard gregexpr function that does exact matching only. Standard

问题 I'm replacing gregexpr with gregexpr2 to detect overlapping matches. When I try. >subSeq 3000-letter "DNAString" instance seq: ACACGTGTTCTATTTTCATTTGCTGACATTTTCTAGTGCATCATTTTTTATTTTATTTTCATT.... gregexpr2("TAAT|ATTA",subSeq) Error in matches[[i]] : subscript out of bounds whereas gregexpr("TAAT|ATTA",subSeq) works fine. What happened? 回答1: It is quite clear if you read gregexpr2 documentation: This is a replacement for the standard gregexpr function that does exact matching only. Standard

问题 I wanted to install "DESeq2" package in R, but it was missing the xml2-config file. I found somewhere that it can be obtained by installing the libxml2 package, but when I tried it gives error that it's not available for R version 3.4.2. Anyone has idea what to do? 回答1: You can install the dev version: devtools::install_github("r-lib/xml2") 回答2: After running what @amarchin wrote it didn't work instantly but R suggested to install libxml2-dev. So I run: sudo apt-get install libxml2-dev in

问题 I am using the following code to retrieve Gene Symbols from Entrez IDs: library("biomaRt") ensembl <- useMart("ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl", host = "www.ensembl.org") g <- getBM(c("hgnc_symbol"), filters = "entrezgene", c(entrez), ensembl) but I get the following error: Error in value[[3L]](cond): Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down. Traceback: 1. getBM(c

问题 I have a package on Bioconductor and I'm in the process of adding a second vignette to it. I want to link the second vignette to the first vignette, as one vignette is on the general workflow of the package and the second is on fine parameter tuning, for more advanced users. Is there a clean way to do it ? The only related topic that I found is this one : best way to link to a vignette from manual in an R package But it did not really helped me, Thanks for your help, Alexis 回答1: If you're

问题 I downloaded bioconductor and attempted to install a package ("limma") which installed successfully, however when I tried to update bioconductor I keep getting errors relating to invalid compiler options. It seems to be specific to gcc, the gfortran packages install without issue. Here is the output: [xxx]$ su -c 'R' Password: R version 2.15.2 (2012-10-26) -- "Trick or Treat" Copyright (C) 2012 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-redhat-linux-gnu (64