flags {MANOR} | R Documentation |
This data set provides flag
objects that can be applied to arrayCGH
objects in order to normalize them.
data(flags)
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 |
People interested in tools for array-CGH analysis can visit our web-page: http://bioinfo.curie.fr.
Pierre Neuvial, manor@curie.fr.
Institut Curie, manor@curie.fr.
spatial
, norm.arrayCGH
,
flag
, flag.summary
data(flags) ### complete normalization of an arrayCGH object (with spatial gradient): ## Initialize flag$args flag.list1 <- list(local.spatial=local.spatial.flag, global.spatial=global.spatial.flag, spot=spot.flag, SNR=SNR.flag, val.mark=val.mark.flag, unique=unique.flag, amplicon=amplicon.flag, chromosome=chromosome.flag, replicate=replicate.flag) data(spatial) ## Not run: gradient.norm <- norm.arrayCGH(gradient, flag.list=flag.list1, var="LogRatio", FUN=median, na.rm=TRUE) ## End(Not run) print(gradient.norm$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$label <- "Image analysis" ## Not run: edge.norm <- norm.arrayCGH(edge, flag.list=flag.list2, var="LogRatio", FUN=median, na.rm=TRUE) ## End(Not run) print(edge.norm$flags) ## spot-level flag summary (computed by flag.summary)