flag.summary: Summarize information about flags after array normalization

In MANOR: CGH Micro-Array NORmalization

Description

Compute spot-level information (number of flagged spots, normalization parameters), and display it in a convenient way

Usage

## S3 method for class 'arrayCGH'
flag.summary(arrayCGH, flag.list, flag.var="Flag", nflab="not flagged", ...)
## Default S3 method:
flag.summary(spot.flags, flag.list, nflab="not flagged", ...)

Arguments

arrayCGH	an object of type arrayCGH, after normalization by MANOR
flag.list	a list of flags with flag\$char corresponding to the values of spot.flags
flag.var	the name of a variable of arrayCGH\$arrayValues containing information about flags (defaults to Flag)
var	the name of a variable of arrayCGH\$cloneValues containing signal values (defaults to LogRatio)
spot.flags	a character vector containing information about flags
nflab	a character vector providing a legend for "not flagged" spots
...	...

Details

This function is used by the function html.report for the generation of an HMTL report of the normalization step. It can also be used by itself.

Value

A data.frame data.frame with 4 columns:

name	flag character
label	flag label
arg	first numeric argument of flag\$FUN
count	number of flagged spots

Note

People interested in tools for array-CGH analysis can visit our web-page: http://bioinfo.curie.fr.

Author(s)

Pierre Neuvial, [e-mail].

See Also

html.report, flag

Examples

data(spatial)
data(flags)
flag.list <- list(spatial=local.spatial.flag, spot=spot.corr.flag,
ref.snr=ref.snr.flag, dapi.snr=dapi.snr.flag, rep=rep.flag,
unique=unique.flag) 
flag.list$spatial$args <- alist(var="ScaledLogRatio", by.var=NULL,
nk=5, prop=0.25, thr=0.15, beta=1, family="symmetric") 
flag.list$spot$args <- alist(var="SpotFlag")
flag.list$spot$char <- "O"
flag.list$spot$label <- "Image analysis"

## normalize arrayCGH
## Not run: edge.norm <- norm(edge, flag.list=flag.list,
var="LogRatio", FUN=median, na.rm=TRUE)
## End(Not run) 
fs <- flag.summary(edge.norm, flag.list=flag.list, flag.var="Flag")

print("Flag and normalization parameters summary")
print(fs)

MANOR documentation built on Nov. 8, 2020, 6:52 p.m.