R/utils.R

In Nanostring-Biostats/NanoStringNCTools: NanoString nCounter Tools

Defines functions sAtMost sAtLeast sBelow sAbove fAtMost fAtLeast fBelow fAbove sIntScale sIntCenter sIntThresh fIntScale fIntCenter fIntThresh sScale sCenter sThresh fScale fCenter fThresh .safe.as.integer strwrpr log2t logt

Documented in fAbove fAtLeast fAtMost fBelow fCenter fIntCenter fIntScale fIntThresh fScale fThresh log2t logt sAbove sAtLeast sAtMost sBelow sCenter sIntCenter sIntScale sIntThresh sScale sThresh

logt <- function(x, thresh = 0.5) {
    if (min(x, na.rm = TRUE) < thresh) {
        x[!is.na(x) & x >= 0 & x < thresh] <- thresh
    }
    log(x)
}
log2t <- function(x, thresh = 0.5) {
    if (min(x, na.rm = TRUE) < thresh) {
        x[!is.na(x) & x >= 0 & x < thresh] <- thresh
    }
    log2(x)
}
strwrpr <- function(x) {
    if (!grepl(" ", x)) {
        x <- gsub("(.{16})", "\\1 ", x)
    }
    paste(strwrap(x, 16), collapse = "\n")
}
.safe.as.integer <- function(x) {
    x <- round(x)
    storage.mode(x) <- "integer"
    x
}
fThresh <- function(x, STATS) sweep(x, 1L, STATS, FUN = "pmax")
fCenter <- function(x, STATS) sweep(x, 1L, STATS, FUN = "-")
fScale <- function(x, STATS) sweep(x, 1L, STATS, FUN = "/")
sThresh <- function(x, STATS) sweep(x, 2L, STATS, FUN = "pmax")
sCenter <- function(x, STATS) sweep(x, 2L, STATS, FUN = "-")
sScale <- function(x, STATS) sweep(x, 2L, STATS, FUN = "/")
fIntThresh <- function(x, STATS) .safe.as.integer(sweep(x, 1L, STATS, FUN = "pmax"))
fIntCenter <- function(x, STATS) .safe.as.integer(sweep(x, 1L, STATS, FUN = "-"))
fIntScale <- function(x, STATS) .safe.as.integer(sweep(x, 1L, STATS, FUN = "/"))
sIntThresh <- function(x, STATS) .safe.as.integer(sweep(x, 2L, STATS, FUN = "pmax"))
sIntCenter <- function(x, STATS) .safe.as.integer(sweep(x, 2L, STATS, FUN = "-"))
sIntScale <- function(x, STATS) .safe.as.integer(sweep(x, 2L, STATS, FUN = "/"))
fAbove <- function(x, STATS) sweep(x, 1L, STATS, FUN = ">")
fBelow <- function(x, STATS) sweep(x, 1L, STATS, FUN = "<")
fAtLeast <- function(x, STATS) sweep(x, 1L, STATS, FUN = ">=")
fAtMost <- function(x, STATS) sweep(x, 1L, STATS, FUN = "<=")
sAbove <- function(x, STATS) sweep(x, 2L, STATS, FUN = ">")
sBelow <- function(x, STATS) sweep(x, 2L, STATS, FUN = "<")
sAtLeast <- function(x, STATS) sweep(x, 2L, STATS, FUN = ">=")
sAtMost <- function(x, STATS) sweep(x, 2L, STATS, FUN = "<=")