# Save barcode tables downloaded from TCGA
library(dplyr)
options(stringsAsFactors = FALSE)
center.types <- c(BCR = "Biospecimen Core Resource",
GCC = "Genome Characterization Center",
CGCC = "Cancer Genomic Characterization Center",
GSC = "Genome Sequencing Center",
GDAC = "Genome Data Analysis Center",
DCC = "Data Coordinating Center",
COM = "Commercial Center") # My best guess for COM
analytes <- c(D = "DNA",
G = "WGA.genomeplex",
H = "miRNA",
R = "RNA",
T = "totalRNA",
W = "WGA.replig",
X = "WGA.replig2")
tables <- dir("data-raw/barcode-tables", full.names = TRUE)
names(tables) <- sub(".csv", "", basename(tables))
tables <- lapply(tables, read.csv, na.strings = "", colClasses = "character")
logicals <- c("Yes" = TRUE, "No" = FALSE)
tables$dataType$Available <- tables[tables$dataType$Available]
tables$platformCode$Available <- tables[tables$platformCode$Available]
lower_names <- function(x) structure(x, names = tolower(names(x)))
tables <- lapply(tables, lower_names)
.bc <- list(
tss = rename(tables$tissueSourceSite,
code = tss.code,
tss = source.site,
disease = study.name),
center = rename(tables$centerCode,
center.type.short = center.type,
center.name.short = short.name,
center.name.long = display.name) %>%
mutate(center.type.long = center.types[center.type.short]) %>%
select(-center.name) %>% # Remove center URL
select(code, contains("name"), contains("type")),
disease = rename(tables$diseaseStudy,
disease.short = study.abbreviation,
disease.long = study.name),
analyte = rename(tables$portionAnalyte,
analyte.long = definition) %>%
mutate(analyte.short = analytes[code]),
sample = rename(tables$sampleType,
sample.short = short.letter.code,
sample.long = definition)
)
save(.bc, file = "R/sysdata.rda")
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.