data-raw/get_data.R

In pereiramemo/bgcpred: Biosynthetic gene cluster abundance prediction models

# -----------------------------------------------------------------------------
# Deff. Env -------------------------------------------------------------------
# -----------------------------------------------------------------------------

URL_PREFIX <- "https://github.com/pereiramemo/BiG-MEx/wiki/files/"

# -----------------------------------------------------------------------------
# Class2dom -------------------------------------------------------------------
# -----------------------------------------------------------------------------

class2dom <- read.table("data/class2domain.csv", header=T, sep=",", row.names = 1)

# -----------------------------------------------------------------------------
# Get Marine Models -----------------------------------------------------------
# -----------------------------------------------------------------------------

URL <- paste(URL_PREFIX,"OMs_model.RData", sep = "")

x <- load(url(URL))
OMs_model <- get(x)

# -----------------------------------------------------------------------------
# Get Infant Gut Models -------------------------------------------------------
# -----------------------------------------------------------------------------

URL <- paste(URL_PREFIX,"IGD_model.RData", sep = "")

x <- load(url(URL))
IGD_model <- get(x)

# -----------------------------------------------------------------------------
# Get Stool models ------------------------------------------------------------
# -----------------------------------------------------------------------------

URL <- paste(URL_PREFIX,"HMP_GIT_model.RData", sep = "")

x <- load(url(URL))
HMP_GIT_model <- get(x)

# -----------------------------------------------------------------------------
# Get Oral models -------------------------------------------------------------
# -----------------------------------------------------------------------------

URL <- paste(URL_PREFIX,"HMP_Oral_model.RData", sep = "")

x <- load(url(URL))
HMP_Oral_model <- get(x)

# -----------------------------------------------------------------------------
# Get Urogenital models -------------------------------------------------------
# -----------------------------------------------------------------------------

# URL <- paste(URL_PREFIX,"HMP_UGT_model.RData", sep = "")
#
# x <- load(url(URL))
# HMP_UGT_model <- get(x)

# -----------------------------------------------------------------------------
# Get General models ----------------------------------------------------------
# -----------------------------------------------------------------------------

URL <- paste(URL_PREFIX,"General_model.RData", sep = "")

x <- load(url(URL))
General_model <- get(x)

# -----------------------------------------------------------------------------
# Get Streptomyces models -----------------------------------------------------
# -----------------------------------------------------------------------------

URL <- paste(URL_PREFIX,"Streptomyces_model.RData", sep = "")

x <- load(url(URL))
Streptomyces_model <- get(x)

# -----------------------------------------------------------------------------
# Save data -------------------------------------------------------------------
# -----------------------------------------------------------------------------

devtools::use_data(class2dom,
                   OMs_model,
                   IGD_model,
                   HMP_GIT_model,
                   HMP_Oral_model,
                   General_model,
                   Streptomyces_model,
                   internal = FALSE,
                   overwrite = TRUE)