flags {MANOR} | R Documentation

## 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)

### Note

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

### Author(s)

Pierre Neuvial, manor@curie.fr.

### Source

Institut Curie, manor@curie.fr.

### 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)

[Package MANOR version 1.56.0 Index]