MANOR (version 1.44.0)

flag.summary: Summarize information about flags after array normalization

Description

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

Usage

"flag.summary"(arrayCGH, flag.list, flag.var="Flag", nflab="not flagged", ...)
"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

...

...

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

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.

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)