Martin Morgan mtmorgan
mtmorgan
/ cigarAlign.R
Created
November 13, 2012 17:32
Represent aligned DNA sequences as a DNAStringSet based on position and CIGAR
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| library(Rsamtools) | |
| .cigarAlignInput <- | |
| function(file, param, what) | |
| { | |
| result <- readBamGappedAlignments(file, param=param) | |
| names(mcols(result))[names(mcols(result)) == what] <- "what" | |
| result | |
| } |
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| library(shiny) | |
| library(org.Hs.eg.db) | |
| library(org.Mm.eg.db) | |
| library(org.Dm.eg.db) | |
| db <- c(Human="org.Hs.eg.db", Mouse="org.Mm.eg.db", | |
| Drosophila="org.Dm.eg.db") | |
| map <- lapply(db, function(elt) tryCatch({ | |
| library(elt, quietly=TRUE, character.only=TRUE) |
mtmorgan
/ ucscAnnotateGenome.R
Created
September 29, 2014 02:02
Retrieve UCSC genomes() and their latin bionomial by scraping UCSC web pages, and translate these to NCBI taxonomyId through entrez eutils calls
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| loadNamespace("rtracklayer") | |
| loadNamespace("XML") | |
| .organismToTaxid <- function(organism=character()) | |
| { | |
| ## query NCBI for taxonomy ID | |
| .eutils <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils" | |
| ## 1. ids | |
| uorganism <- unique(organism[!is.na(organism)]) |
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| ## compatibility | |
| if (!exists("lengths")) | |
| lengths <- function(x) vapply(x, length, integer(1)) | |
| ## | |
| ## methods | |
| ## | |
| .S4methodsForClass <- |
mtmorgan
/ GSE62944_TCGA_Rusbread_featureCounts.R
Last active
August 29, 2015 14:17
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| ## Imports: GEOquery, Biobase | |
| acc <- "GSE62944" | |
| if (!file.exists(acc)) | |
| GEOquery::getGEOSuppFiles(acc) | |
| setwd(acc) | |
| clinvar <- local({ | |
| message("clinvar") | |
| fl <- "GSE62944_TCGA_20_420_Clinical_Variables_7706_Samples.txt.gz" |
mtmorgan
/ readKallisto.R
Last active
December 4, 2017 11:51
read kallisto RNA-seq quantification into R / Bioconductor data structures
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| .require <- | |
| function(pkg) | |
| { | |
| withCallingHandlers({ | |
| suppressPackageStartupMessages({ | |
| require(pkg, character.only=TRUE, quietly=TRUE) | |
| }) | |
| }, warning=function(w) { | |
| invokeRestart("muffleWarning") | |
| }) || { |
mtmorgan
/ gist:bd147505b89e42a151f9
Created
June 24, 2015 18:54
dplyr / SummarizedExperiment compatibility layer -- half baked
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| ## dplyr compatibility | |
| as.data.frame.RangedSummarizedExperiment <- | |
| function(x, row.names=NULL, optional=FALSE, ...) | |
| { | |
| colData <- colData(x) | |
| rownames(colData) <- NULL | |
| cbind(as.data.frame(rowRanges(x)[as.vector(row(x))]), | |
| as.data.frame(colData[as.vector(col(x)),, drop=FALSE]), | |
| sapply(assays(x), as.vector)) |
mtmorgan
/ phred2ASCIIOffset.R
Created
March 15, 2016 14:44
Translate integer or ASCII character fastq phred score encodings to integer offsets useful in Rsamtools
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| .ascii_offset <- function() | |
| setNames(33:126 - 33L, strsplit(rawToChar(as.raw(33:126)), "")[[1]]) | |
| .phred2ascii_int <- | |
| function(x, scheme) | |
| { | |
| ## See https://en.wikipedia.org/wiki/FASTQ_format#Encoding | |
| ascii <- .ascii_offset() | |
| switch(scheme, "Illumina 1.8+" = { | |
| ## L - Illumina 1.8+ Phred+33, raw reads typically (0, 41) |
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| #' Query DisGeNET disease / gene database | |
| #' | |
| #' Based on a script by jpinero@imim.es, retrieved from | |
| #' http://www.disgenet.org/ds/DisGeNET/scripts/disgenet.R on 7 April, | |
| #' 2016. This version is meant for interactive use within an R | |
| #' session, and makes a single query to DisGeNET rather than one query | |
| #' for each input symbol. | |
| #' | |
| #' @param input: character vector of gene or disease identifiers | |
| #' |
mtmorgan
/ grangesToSymbol
Created
July 29, 2016 20:50
Extract ranges of genes, and map ranges to corresponding genes
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| geneRanges <- | |
| function(db, column="ENTREZID") | |
| { | |
| g <- genes(db, columns=column) | |
| col <- mcols(g)[[column]] | |
| genes <- granges(g)[rep(seq_along(g), elementNROWS(col))] | |
| mcols(genes)[[column]] <- as.character(unlist(col)) | |
| genes | |
| } |
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