flag.summary {MANOR} | R Documentation |
Compute spot-level information (number of flagged spots, normalization parameters), and display it in a convenient way
flag.summary.arrayCGH(arrayCGH, flag.list, flag.var="Flag", nflab="not flagged", ...) flag.summary.default(spot.flags, flag.list, nflab="not flagged", ...)
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 |
... |
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.
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 |
People interested in tools for array-CGH analysis can visit our web-page: http://bioinfo.curie.fr.
Pierre Neuvial, manor@curie.fr.
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.arrayCGH(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)