batch.spline {aCGH.Spline}R Documentation

Function for batch processing.

Description

Function for batch processing aCGH data though the "Jspline" method.

Usage

batch.spline(dir, format = "FE", raw=TRUE, robust = TRUE, offset=5, knots=1000,
                ntyp = "percentile", p = 0.68, fact = 4.5, segN = FALSE, 
                sn = 0.75, writeFE = FALSE, QC = FALSE, GFF = FALSE, PDF = FALSE)

Arguments

dir - the directory to process.
format - the type of file format - c("FE", "NIM").
raw - to use raw data or not (TRUE or FALSE).
robust - make the method robust to outliers (TRUE or FALSE).
offset - parameters to set the number of time the knot point will be offset.
knots - the number of knot points to use for spline fitting.
ntyp - type of noise calculation to perform - c("percentile", "derivative", "combined").
p - value between 0 and 1 (the percentile value).
fact - numeric value (the factor by which the noise value will be rised).
segN - option for robust noise calculation (recommended when data contains many outliers e.g. cancer sample) TRUE or FALSE.
sn - value between 0 and 1 - threshold for segmentation (segN).
writeFE - Output a Feature Extraction formatted file (only to be used when processing Agilent FE files).
QC - produce a QC report TRUE or FALSE.
GFF - produce a GFF formatted file TRUE or FALSE.
PDF - produce a PDF containing normalisation figures TRUE or FALSE.

Details

Running this function using defalut parameters (just providing the directory argument) will perform consistantly across a wide range of data qualities.

If method optimisation is required, the number of knot points and offsets can be adjusted along with the various noise estimation parameters.

Value

As default this function outputs one ".temp" formatted file per file processed.

The ".temp" format consists of seven columns:

- Cy5 intensity values.
- Cy3 intensity values.
- Chromosome number.
- Start position.
- Stop position.
- An index.
- A flag.

Note

This function assumes that all "*.txt" files within the target directory are in the specified format.
(Agilent "FeatureExtraction.txt" or Nimblegen "SEG_MNT.txt" files)

Author(s)

Tomas William Fitzgerald

Examples

# batch.spline(".")
# This would run batch processing on the current directory using default settings.


[Package aCGH.Spline version 2.2 Index]