Martin Morgan mtmorgan
mtmorgan
/ gist:bd147505b89e42a151f9
Created
June 24, 2015 18:54
dplyr / SummarizedExperiment compatibility layer -- half baked
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| ## 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
/ readKallisto.R
Last active
December 4, 2017 11:51
read kallisto RNA-seq quantification into R / Bioconductor data structures
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| .require <- | |
| function(pkg) | |
| { | |
| withCallingHandlers({ | |
| suppressPackageStartupMessages({ | |
| require(pkg, character.only=TRUE, quietly=TRUE) | |
| }) | |
| }, warning=function(w) { | |
| invokeRestart("muffleWarning") | |
| }) || { |
mtmorgan
/ GSE62944_TCGA_Rusbread_featureCounts.R
Last active
August 29, 2015 14:17
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| ## 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" |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| ## compatibility | |
| if (!exists("lengths")) | |
| lengths <- function(x) vapply(x, length, integer(1)) | |
| ## | |
| ## methods | |
| ## | |
| .S4methodsForClass <- |
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
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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)]) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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
/ cigarAlign.R
Created
November 13, 2012 17:32
Represent aligned DNA sequences as a DNAStringSet based on position and CIGAR
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| library(Rsamtools) | |
| .cigarAlignInput <- | |
| function(file, param, what) | |
| { | |
| result <- readBamGappedAlignments(file, param=param) | |
| names(mcols(result))[names(mcols(result)) == what] <- "what" | |
| result | |
| } |
NewerOlder