data-raw/Subset-Progenesis.R

In dpritchLibre/PepSAVIms: PepSAVI-MS Data Analysis

# Read mass spectrometry data --------------------------------------------------

# Arg specifications determined by a visual inspection of the csv file.  The
# reason for the nrows argument is b/c the last row of data is incomplete.

progenesis <- read.csv("data-raw/20150427_CLK_BAP_VO_peptide_ion_data.csv",
                       skip=2, row.names=1, nrows=30799, check.names=FALSE)


# Keep m/z, Retention time (min), Mass, and Charge columns, corresponding to the
# 1, 2, 4, and 5-th columns respectively.

# Want to subset to the "intensity, condition 1" fractions: correspond to
# columns 77-111

# Fraction 32 has versions Sample0 and Sample1.  We don't want to use Sample0,
# which corresponds to the 98-th column.

mass_spec <- progenesis[, c(1:2, 4:5, setdiff(77:111, 98))]
names(mass_spec)[ grepl("Sample1", names(mass_spec)) ] <- "20150207_CLK_BAP_VO_32"




# Read bioactivity data --------------------------------------------------------

biomat <- read.csv("data-raw/20160727_VO all active bioactivity data with replicates.csv",
                   row.names=1, check.names=FALSE)
# Some of the names start with an X, remove for consistency
names(biomat) <- c("Modeling region",
                   paste0("20150207_CLK_BAP_VO_", 1:43),
                   "20150207_CLK_BAP_VO_47")

# Create a list with each element a data.frame of the bioactivity observations
# for a given pathogen or cancer cell line.  Each row in the data.frames is a
# replicate, and the columns are bioactivity data for exposure to a fraction.
#
# Note: the E. faecium (ef) data was determined by the laboratory to be faulty,
# so it is not included
region_idx <- 2:45
bioact <- list()
bioact$ec <- biomat[8:10, region_idx]
bioact$bc <- biomat[11:13, region_idx]
bioact$pc <- biomat[14:16, region_idx]
bioact$oc <- biomat[17:19, region_idx]
# bioact$ef <- biomat[20:22, region_idx]
bioact$ab <- biomat[23:25, region_idx]
bioact$pa <- biomat[26:28, region_idx]
bioact$fg <- biomat[29:30, region_idx]



# Save data to RData format ----------------------------------------------------

# Saves mass_spec in the file data/mass_spec.rda and bioact in the file
# data/bioact.rda
devtools::use_data(mass_spec, bioact)