diff --git a/man/grabAccessionData.Rd b/man/grabAccessionData.Rd index f37b457..bd507e4 100644 --- a/man/grabAccessionData.Rd +++ b/man/grabAccessionData.Rd @@ -25,6 +25,7 @@ Get arbitrary metadata from an mzML file by accession number } \examples{ library(RaMS) +\dontshow{data.table::setDTthreads(2)} sample_dir <- system.file("extdata", package = "RaMS") sample_file <- list.files(sample_dir, full.names=TRUE)[3] # Get ion injection time diff --git a/man/grabMSdata.Rd b/man/grabMSdata.Rd index c027e0a..c30f525 100644 --- a/man/grabMSdata.Rd +++ b/man/grabMSdata.Rd @@ -95,6 +95,7 @@ if they are encoded in seconds. } \examples{ library(RaMS) +\dontshow{data.table::setDTthreads(2)} # Extract MS1 data from a couple files sample_dir <- system.file("extdata", package = "RaMS") sample_files <- list.files(sample_dir, full.names=TRUE) diff --git a/man/grabMzmlData.Rd b/man/grabMzmlData.Rd index 4291843..8c1e923 100644 --- a/man/grabMzmlData.Rd +++ b/man/grabMzmlData.Rd @@ -88,6 +88,7 @@ to the user in case per-file optimization (such as peakpicking or additional filtering) is desired before the full data object is returned. } \examples{ +\dontshow{data.table::setDTthreads(2)} sample_file <- system.file("extdata", "LB12HL_AB.mzML.gz", package = "RaMS") file_data <- grabMzmlData(sample_file, grab_what="MS1") \dontrun{ diff --git a/man/grabMzxmlData.Rd b/man/grabMzxmlData.Rd index ad41550..86aecdb 100644 --- a/man/grabMzxmlData.Rd +++ b/man/grabMzxmlData.Rd @@ -81,6 +81,7 @@ exposed to the user in case per-file optimization (such as peakpicking or additional filtering) is desired before the full data object is returned. } \examples{ +\dontshow{data.table::setDTthreads(2)} sample_file <- system.file("extdata", "LB12HL_AB.mzXML.gz", package = "RaMS") file_data <- grabMzxmlData(sample_file, grab_what="MS1") \dontrun{ diff --git a/man/mz_group.Rd b/man/mz_group.Rd index 0fff226..5d087ed 100644 --- a/man/mz_group.Rd +++ b/man/mz_group.Rd @@ -36,6 +36,7 @@ in the m/z vector as the window center, it's often a good idea to first sort the values by decreasing intensity. } \examples{ +\dontshow{data.table::setDTthreads(2)} example_mz_vals <- c(118.0, 118.1, 138.0, 152.0, 118.2, 138.1, 118.1) mz_group(example_mz_vals, ppm = 1) mz_group(example_mz_vals, ppm = 1000) @@ -44,6 +45,7 @@ mz_group(example_mz_vals, ppm = 200000) mz_group(example_mz_vals, ppm = 1000, min_group_size = 2) mz_group(example_mz_vals, ppm = 1000, max_groups = 2) +\dontrun{ sample_dir <- system.file("extdata", package = "RaMS") sample_files <- list.files(sample_dir, full.names=TRUE) msdata <- grabMSdata(sample_files[c(3, 5, 6)], grab_what="MS1") @@ -70,3 +72,4 @@ msdata$MS1[mz\%between\%pmppm(119.0865, 100)] \%>\% mutate(mz_group=mz_group(mz, ppm=5, max_groups = 2)) \%>\% qplotMS1data(facet_col = "mz_group") } +} diff --git a/man/qplotMS1data.Rd b/man/qplotMS1data.Rd index e21c772..6ff0211 100644 --- a/man/qplotMS1data.Rd +++ b/man/qplotMS1data.Rd @@ -44,6 +44,7 @@ name of the associated column to the `color_col` and `facet_col` arguments, respectively. } \examples{ +\dontshow{data.table::setDTthreads(2)} test_df <- expand.grid(rt=rep(1:100, length.out=1000)) test_df$int <- rep(dnorm(seq(-10, 10, length.out=100)), 10)*10+runif(1000) test_df$filename <- rep(LETTERS[1:10], each=100) @@ -55,8 +56,10 @@ qplotMS1data(test_df, color_col="startime", facet_col="startime", facet_args=list(ncol=2, scales="free")) # Using data from the `grabMSdata` function: +\dontrun{ sample_dir <- system.file("extdata", package = "RaMS") sample_files <- list.files(sample_dir, full.names=TRUE) msdata <- grabMSdata(sample_files[c(3, 5, 6)], grab_what="MS1") qplotMS1data(msdata$MS1[mz\%between\%pmppm(118.0865)]) } +}