bslnoff: Baseline Substraction
In PROcess: Ciphergen SELDI-TOF Processing

Description Usage Arguments Value Author(s) Examples

This function estimates the baseline and then removes baseline from the raw spectrum.

1	bslnoff(f, breaks = 200, qntl = 0, method = c("loess", "approx"), bw = 0.005, plot = FALSE, ...)

`f`	a matrix with M/Z values in the first column and intensities in the second column
`breaks`	number of breaks set to M/Z values for finding the local minima or points below a centain quantile of intensities; breaks -1 equally spaced intervals on the log M/Z scale.
`qntl`	if 0, find local minima; if >0 find intensities < qntl*100th quantile locally.
`method`	"loess" or "approx" (linear interpolation).
`bw`	the bandwidth to be passed to loess.
`plot`	TRUE or FALSE, if true, it will plot the raw spectrum, theestimated baseline and the baseline substracted spectrum.
`...`	Further parameters that get passed on to plot.

a matrix of two columns: the first column being the M/Z values same as the input, and the second column being the baseline substracted spectra.

Xiaochun Li

fdat <- system.file("Test", package = "PROcess")
fs <- list.files(fdat, pattern="\\.*csv\\.*", full.names=TRUE)
f1 <- read.files(fs[1])
fcut <- f1[f1[,1]>0,]
bseoff <-bslnoff(fcut,method="loess",plot=TRUE, bw=0.1)
title(basename(fs[1]))