flags: Examples of flag objects to apply to CGH arrays

In MANOR: CGH Micro-Array NORmalization

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)

Note

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

Author(s)

Pierre Neuvial, [e-mail].

Source

Institut Curie, [e-mail].

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)

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