## ----style, echo = FALSE, results = 'asis', message=FALSE---------------- BiocStyle::markdown() ## ----env, echo=FALSE, message=FALSE-------------------------------------- suppressPackageStartupMessages(library("AnnotationHub")) suppressPackageStartupMessages(library("ProteomicsAnnotationHubData")) suppressPackageStartupMessages(library("mzR")) ## ----ahinit-------------------------------------------------------------- library("AnnotationHub") ah <- AnnotationHub() ah ## ----provider------------------------------------------------------------ query(ah, "PRIDE") ## ----title--------------------------------------------------------------- query(ah, "PXD000001") ## ----ah49008------------------------------------------------------------- ah["AH49008"] ## ----rawmsdata----------------------------------------------------------- library("mzR") rw <- ah[["AH49008"]] rw ## ----msdataplot---------------------------------------------------------- plot(peaks(rw, 1), type = "h", xlab = "M/Z", ylab = "Intensity") ## ----availablepahd------------------------------------------------------- library("ProteomicsAnnotationHubData") availableProteomicsAnnotationHubData ## ---- echo=FALSE--------------------------------------------------------- cat(readLines(dir(system.file("extdata", package = "ProteomicsAnnotationHubData"), full.names = TRUE, pattern = "PXD000001.dcf"))[10:30], sep = "\n") ## ------------------------------------------------------------------------ writePahdTemplate() ## ----PXD000001.dcf, echo=FALSE------------------------------------------- f <- list.files(system.file("extdata", package = "ProteomicsAnnotationHubData"), full.names = TRUE, pattern = "PXD000001.dcf") cat(readLines(f)[10:30], sep = "\n") ## ----providers, echo=FALSE----------------------------------------------- tab <- do.call(rbind, ProteomicsAnnotationHubData:::ProteomicsAnnotationHubDataProviders) knitr::kable(tab, row.names = FALSE) ## ----tags, echo=FALSE---------------------------------------------------- ProteomicsAnnotationHubData:::ProteomicsAnnotationHubDataTags ## ----PXD000001.R, echo=FALSE--------------------------------------------- f <- list.files(system.file("scripts", package = "ProteomicsAnnotationHubData"), full.names = TRUE, pattern = "PXD000001.R") cat(readLines(f)[1:4], sep = "\n") ## ---- eval=FALSE--------------------------------------------------------- # setClass("mzRpwizResource", contains="AnnotationHubResource") # setMethod(".get1", "mzRpwizResource", # function(x, ...) # { # .require("mzR") # yy <- cache(.hub(x)) # mzR::openMSfile(yy, backend = "pwiz") # }) ## ---- eval=FALSE--------------------------------------------------------- # setClass("mzRidentResource", contains="AnnotationHubResource") # setMethod(".get1", "mzRidentResource", # function(x, ...) # { # .require("mzR") # yy <- cache(.hub(x)) # mzR::openIDfile(yy) # }) ## ---- eval=FALSE--------------------------------------------------------- # setClass("MSnSetResource", contains="RdaResource") # setMethod(".get1", "MSnSetResource", # function(x, ...) # { # .require("MSnbase") # callNextMethod(x, ...) # }) ## ---- eval=FALSE--------------------------------------------------------- # setClass("AAStringSetResource", contains="AnnotationHubResource") # setMethod(".get1", "AAStringSetResource", # function(x, ...) # { # .require("Biostrings") # yy <- cache(.hub(x)) # Biostrings::readAAStringSet(yy) # })