bias: WACA bias computation for a probe series
In cghRA: Array CGH Data Analysis and Visualization

Description Usage Arguments Value Author(s) References See Also

This function computes the various probe-dependant biases used by the Waves aCGH Correction Algorithm (WACA), in order to apply this correction to CGH arrays using these probes.

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  bias(chromFiles, probeChrom, probeStarts, probeEnds,
    chromPattern = "^(.+)\\.[^\\.]+$", fragSites = c(AluI = "AG|CT", RsaI = "GT|AC"),
    digits = 6, verbose = 1)

`chromFiles`	Character vector, paths to chromosome sequences (a single fasta file for each chromosome).
`probeChrom`	`character` vector, for each probe its chromosome location.
`probeStarts`	`integer` vector, for each probe its chromosome starting position (first base is 1, starting position is comprised in the probe).
`probeEnds`	`integer` vector, for each probe its chromosome ending position (first base is 1, ending position is comprised in the probe).
`chromPattern`	Single character value, a regular expression to be used for chromosome name extraction from `chromFiles`. It needs to capture a single value for replacement, default value will use the base names of the files without extension as chromosome names.
`fragSites`	Named character vector describing the restriction enzymes used for the CGH experiment. Restriction sites are described in upper cases, with a pipe at the fragmentation position (see the default value for an example). Only A, C, G and T letters allowed.
`digits`	Single integer value, to be passed to `round` for all bias values.
`verbose`	Single integer value, whether to print diagnostic `message`s or not.

Returns a double matrix, with probes in rows and the following columns :

`wGC150`	GC frequency in a window of 150 kb on each side of the probe
`wGC500`	GC frequency in a window of 500 kb on each side of the probe
`wGCprobe`	GC frequency in the probe sequence
`wGCfrag`	GC frequency in the fragment holding the probe
`wFragSize`	Size (in bp) of the fragment holding the probe