Levi Waldron lwaldron
lwaldron
/ MAE_notquite.r
Created
March 18, 2016 15:59
An example of a MultiAssayExperiment setup with sample naming problems
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| library(MultiAssayExperiment) | |
| load('nci60dat.rda') | |
| rnadat <- Biobase::ExpressionSet(assayData=rna.arraydat) | |
| proteinMSdat <- Biobase::ExpressionSet(assayData=protein.ms.arraydat) | |
| deepProteinMSdat <- Biobase::ExpressionSet(assayData=deep.protein.ms.arraydat) | |
| kinaseProteinMSdat <- Biobase::ExpressionSet(assayData=kinase.protein.ms.arraydat) | |
| ExpList <- list( |
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| library(Biobase) | |
| library(MultiAssayExperiment) | |
| patient.data <- data.frame(sex=c("M", "F", "M", "F"), | |
| age=38:41, | |
| row.names=c("Jack", "Jill", "Bob", "Barbara")) | |
| arraydat <- matrix(seq(101, 108), ncol=4, | |
| dimnames=list(c("ENST00000294241", "ENST00000355076"), | |
| c("array1", "array2", "array3", "array4"))) | |
| arraypdat <- as(data.frame(slope53=rnorm(4), | |
| row.names=c("array1", "array2", "array3", |
lwaldron
/ metaphlantaxa.R
Created
August 7, 2017 22:51
Write a one-column table of all metaphlan2 taxa at all levels of taxonomy
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| library(curatedMetagenomicData) | |
| newicklabs <- getMetaphlanTree(simplify=FALSE)$tip.label | |
| delims <- paste0("\\|", c("p", "c", "o", "f", "g", "s"), "__.+") | |
| res <- lapply(delims, function(x) sub(x, "", newicklabs)) | |
| res <- unique(unlist(res)) | |
| res <- c(res, grep("s__", newicklabs, val=TRUE)) | |
| res <- sort(res) | |
| res <- grep("GCF", res, invert=TRUE, val=TRUE) | |
| res <- grep("noname$", res, invert = TRUE, value = TRUE) | |
| write.table(res, file="~/Downloads/metaphlantaxa.tsv", row.names=FALSE, col.names = FALSE) |
lwaldron
/ FIMMdose-viability.R
Last active
December 4, 2017 14:48
Some code to provide some dose-viability data to play with:
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| library(PharmacoGx) | |
| fimm <- downloadPSet("FIMM") | |
| slotNames(fimm) | |
| names(fimm@sensitivity) | |
| head(fimm@sensitivity$info) | |
| head(fimm@sensitivity$profiles) | |
| fimm@sensitivity$n[1:5, 1:5] | |
| class(fimm@sensitivity$raw) |
lwaldron
/ gist:4137c0c4fe215590a35a874f3a0af04b
Last active
December 21, 2017 01:31
wideFormat() with experimentColDataCols
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| library(SummarizedExperiment) | |
| library(MultiAssayExperiment) | |
| example("MultiAssayExperiment", echo=FALSE) | |
| myMultiAssayExperiment[[1]] <- SummarizedExperiment(assays=exprs(myMultiAssayExperiment[[1]]), colData=pData(myMultiAssayExperiment[[1]])) | |
| myMultiAssayExperiment[[2]] <- SummarizedExperiment(myMultiAssayExperiment[[2]], colData=DataFrame(slope53=1:5)) | |
| myMultiAssayExperiment[[3]] <- SummarizedExperiment(myMultiAssayExperiment[[3]]) | |
| colData(myMultiAssayExperiment) | |
| colData(myMultiAssayExperiment[[1]]) | |
| colData(myMultiAssayExperiment[[2]]) |
lwaldron
/ installpkgs.R
Created
February 16, 2018 05:19
Install packages for Thomas Carroll ATAC-seq NYC R/Bioconductor meet-up
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| mypkgs <- rownames(installed.packages()) | |
| if (!require("BiocInstaller")) { | |
| source("http://www.bioconductor.org/biocLite.R") | |
| biocLite(ask = FALSE) | |
| } | |
| if (!require("devtools")) | |
| biocLite("devtools", ask = FALSE) |
lwaldron
/ downloadessentials.R
Created
February 16, 2018 05:27
Download essential files for Thomas Carroll ATAC-seq NYC R/Bioconductor meet-up
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| urls <- c("https://s3.amazonaws.com/rubioinformatics/ATAC_Workshop/ATAC_Data/ATAC_BAM/Sorted_ATAC_50K_2.bam", | |
| "https://s3.amazonaws.com/rubioinformatics/ATAC_Workshop/ATAC_Data/ATAC_BAM/Sorted_ATAC_50K_2.bam.bai", | |
| "https://s3.amazonaws.com/rubioinformatics/ATAC_Workshop_Essential.zip") | |
| for (url in urls) | |
| download.file(url, destfile = basename(url)) |
lwaldron
/ CompareBedFiles.R
Created
February 27, 2018 22:06
Comparing two exome sequencing capture kits
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| url1 <- "https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_nextera/nexterarapidcapture/nexterarapidcapture_exome_targetedregions.bed" | |
| url2 <- "https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_nextera/nexterarapidcapture/nexterarapidcapture_expandedexome_targetedregions.bed" | |
| library(rtracklayer) | |
| rapidgr <- import(url1, genome="hg19") | |
| expandedgr <- import(url2, genome="hg19") | |
| library(GenomicRanges) | |
| table(countOverlaps(rapidgr, expandedgr)) |
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| ## A big SE | |
| library(curatedMetagenomicData) | |
| library(SummarizedExperiment) | |
| library(tidyr) | |
| library(ape) | |
| simplifynodes <- TRUE | |
| makeTaxTable <- function(fullnames){ |
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| library(curatedMetagenomicData) | |
| library(SummarizedExperiment) | |
| library(tidyr) | |
| library(ape) | |
| simplifynodes <- TRUE | |
| makeTaxTable <- function(fullnames){ | |
| taxonomic.ranks <- c("Kingdom", "Phylum", "Class", "Order", | |
| "Family", "Genus", "Species", "Strain") |
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