fdr.spatial2 {OLIN} | R Documentation |
This function assesses the significance of spatial bias by a one-sided random permutation test. This is achieved by comparing the observed average values of logged fold-changes within a spot's spatial neighbourhood with an empirical distribution generated by random permutation. The significance of spatial bias is given by the false discovery rate.
fdr.spatial2(object,delta=2,N=100,av="median",edgeNA=FALSE)
object |
object of class marrayRaw or marrayNorm |
delta |
integer determining the size of spot neighbourhoods
((2*delta+1)x(2*delta+1) ). |
N |
number of random permutations performed for generation of empirical background distribution |
av |
averaging of M within neighbourhood by
mean or median (default) |
edgeNA |
treatment of edges of array: For edgeNA=TRUE ,
the significance of a neighbourhood (defined by a sliding window) is set to NA,
if the neighbourhood extends over the edges of the matrix. |
The function fdr.spatial2.Rd
is basically the same as fdr.spatial
,
but differs in its input and output formats.
Details about the functionality can be found
at fdr.spatial
.
Two list of vectors containing the false discovery rates for positive (FDRp
)
and negative (FDRn
) deviations of
median/mean of M
of the spot's neighbourhood is produced. Each
vector contains the false discovery values for one array.
This function will be fused with fdr.spatial
in future versions using S4-style methods.
Matthias E. Futschik (http://itb.biologie.hu-berlin.de/~futschik)
p.spatial
, fdr.int
, sigxy.plot
,
# To run these examples, delete the comment signs before the commands. # # LOADING DATA # data(sw) # # CALCULATION OF SIGNIFICANCE OF SPOT NEIGHBOURHOODS # For this illustration, N was chosen rather small. For "real" analysis, it should be larger. # FDR <- fdr.spatial2(sw,delta=2,N=10,av="median",edgeNA=TRUE) # # SIGNIFICANCE PLOTS OF ARRAY 1 # sigxy.plot2(sw[,1],FDR$FDRp[[1]],FDR$FDRn[[1]],color.lim=c(-5,5),main="FDR") # SIGNIFICANCE PLOTS OF ARRAY 3 # sigxy.plot2(sw[,3],FDR$FDRp[[3]],FDR$FDRn[[3]],color.lim=c(-5,5),main="FDR") #