Nothing
convert_annotation_vector <- function(x, how, what, conc) {
peptides2vector <- function(ids) {
ids <- vapply(ids, paste0, "", collapse = "-")
ifelse(nzchar(ids), ids, NA_character_)
}
create_matrix <- function(x, ids, what, conc) {
x <- as.matrix(x)
colnames(x) <- RESERVED_NAMES[["value"]]
if (L(conc))
x <- cbind(x,
Concentration = substrate_info(rownames(x), "concentration"))
switch(what,
peptide = structure(.Data = cbind(x, collect(ids)),
comment = peptides2vector(ids)),
structure(.Data = cbind(x, collect(web_query(ids, what))), comment = ids)
)
}
create_dataframe <- function(x) {
x <- structure(.Data = as.data.frame(x), comment = comment(x))
names(x) <- make.names(names(x))
for (i in seq_along(x))
if (all(x[, i] %in% c(0, 1, NA_real_)))
x[, i] <- as.factor(as.logical(x[, i]))
x
}
ids <- substrate_info(names(x), what)
case(match.arg(how, c("ids", "values", "data.frame")),
data.frame = create_dataframe(create_matrix(x, ids, what, conc)),
ids = {
switch(what, peptide = ids <- peptides2vector(ids))
structure(.Data = x, names = ids, concentration = if (L(conc))
unname(substrate_info(names(x), "concentration"))
else
NULL, comment = names(x))
},
values = create_matrix(x, ids, what, conc)
)
}
check_mcp_sep <- function(sep) {
if (!is.character(sep) || nchar(sep <- sep[[1L]]) != 1L)
stop("'sep' must be a single character")
sep
}
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