MANOR (version 1.44.0)

flags: Examples of flag objects to apply to CGH arrays

Description

This data set provides flag objects that can be applied to arrayCGH objects in order to normalize them.

Usage

data(flags)

Format

These flag objects typically take part to a normalization process:

	amplicon.flag
flags spots with high log-ratios (temp flag)
chromosome.flag	flags spots located on sexual chromosomes (named "X" and "Y")
	control.flag
flag control spots
global.spatial.flag	corrects arrayCGH from global spatial trend on the array
	local.spatial.flag
flags spots belonging to local spatial bias zones on the array
num.chromosome.flag	flags spots located on sexual chromosomes (named 23 and 24)
	position.flag
flag spots with no available genome position
replicate.flag	flag spots with poor within-clone-replicate consitency
	ref.snr.flag
flags spots with low signal to noise ratio for reference
dapi.snr.flag	flags spots with low signal to noise ratio for DAPI
	SNR.flag
flags spots with low signal to noise ratio
spot.corr.flag	flags spots with low correlation coefficient after image analysis
	spot.flag
flags spots excluded by the image analysis software
unique.flag	exclude last non-flagged spot of a clone
	val.mark.flag
flags spots corresponding to bad quality clones
intensity.flag	corrects for an intensity effect (using loess regression)

Source

Institut Curie, .

See Also

spatial, norm.arrayCGH, flag, flag.summary

Examples

data(flags)

### complete normalization of an arrayCGH object (with spatial gradient):
## Initialize flag$args

flag.list1 <- list(local.spatial=local.spatial.flag,
  global.spatial=global.spatial.flag, spot=spot.flag, SNR=SNR.flag,
  val.mark=val.mark.flag, unique=unique.flag,
  amplicon=amplicon.flag, chromosome=chromosome.flag,
  replicate=replicate.flag)

data(spatial)
## Not run: gradient.norm <- norm(gradient, flag.list=flag.list1,
# var="LogRatio", FUN=median, na.rm=TRUE)## End(Not run)
print(gradient.norm$flags) ## spot-level flag summary (computed by flag.summary)

### complete normalization of an arrayCGH object (with local spatial bias):
## Initialize flag$args

flag.list2 <- 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.list2$spatial$args <- alist(var="ScaledLogRatio", by.var=NULL,
nk=5, prop=0.25, thr=0.15, beta=1, family="symmetric") 
flag.list2$spot$args <- alist(var="SpotFlag")
flag.list2$spot$char <- "O"
flag.list2$spot$label <- "Image analysis"

## Not run: edge.norm <- norm(edge, flag.list=flag.list2,
# var="LogRatio", FUN=median, na.rm=TRUE)## End(Not run) 
print(edge.norm$flags) ## spot-level flag summary (computed by flag.summary)