rmBaseline: Baseline Correction

In HTDA: HTDA (High Throughput Data Analysis)

Description

This function we have exported from PROcess package with a little modification.

Usage

rmBaseline(fldr, bseoffrda = NULL, breaks = 200, qntl = 0, method = "loess", bw = 0.1, SpecNames = list.files(fldr, pattern = "\.*csv\.*"))

Arguments

fldr
bseoffrda
breaks
qntl
method
bw
SpecNames

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (fldr, bseoffrda = NULL, breaks = 200, qntl = 0, method = "loess", 
    bw = 0.1, SpecNames = list.files(fldr, pattern = "\\.*csv\\.*")) 
{
    fs <- list.files(fldr, pattern = "\\.*csv\\.*", full.names = T)
    n <- length(fs)
    par(mfrow = c(3, 3))
    for (j in 1:n) {
        f1 <- read.files(fs[j])
        fcut <- f1[f1[, 1] > 0, ]
        bseoff <- PROcess::bslnoff(fcut, breaks = breaks, qntl = qntl, 
            method = method, plot = TRUE, bw = bw)
        if (j > 1) 
            bseoffM <- cbind(bseoffM, bseoff[, 2])
        else bseoffM <- bseoff[, 2]
    }
    dimnames(bseoffM) <- list(signif(bseoff[, 1], 6), SpecNames)
    if (!is.null(bseoffrda)) 
        save(list = bseoffM, file = bseoffrda)
    bseoffM
  }

HTDA documentation built on May 2, 2019, 4:53 p.m.