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# The purpose of this script is to demonstrate how the e_data, f_data, and
# e_meta data frames were created. It should NOT be rerun because the data sets
# in pmartRdata will change over time and this will lead to errors in the unit
# tests.
# Generate data to test the as.pepData function. -------------------------------
# Load necessary libraries.
library (pmartRdata)
# Load the peptide data objects.
data("pep_edata")
data("pep_fdata")
data("pep_emeta")
# Take a small subset of the rows in pep_edata and pep_emeta to use for testing.
edata <- pep_edata[1:150, ]
# Find all rows in emeta that match the Mass_Tag_IDs from edata. These IDs will
# be used to subset the full emeta object.
id_idx <- which(pep_emeta$Mass_Tag_ID %in% edata$Mass_Tag_ID)
emeta <- pep_emeta[id_idx, ]
# Remove factor levels from emeta variables. This greatly reduces the size of
# the .RData file.
emeta$Protein <- as.character(emeta$Protein)
emeta$Peptide_Sequence <- as.character(emeta$Peptide_Sequence)
# Keep a copy of the original pep_fdata data frame.
fdata <- pep_fdata
# save(edata,
# fdata,
# emeta,
# file = '~/pmartR/inst/testdata/little_pdata.RData')
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