movbin {reb} | R Documentation |
This function analyzes ordered data series to identify regional biases using an moving (running) approximated binomial test.
movbin(v,span=NULL,summarize=mean)
v |
data vector |
span |
numeric vector. Each element is used to define
the number of points to include when the approximated binomial test
is applied to v . While mixed for the defaults, the span can
be specified as fraction of the observation or actual sizes, but
not a mixture - defaults to: seq(25,length(v)*.3,by=5) |
summarize |
function that is used to summarize the results from
multiple spans. if NULL, a matrix with length(span) rows
and length(v) columns is returned. |
movbin
applies a moving binomial test to sequential windows of
elements of v
. Within each span a z-score from an approximated
binomial is computed such that z=(2*r - n)/sqrt(n)
where
r
is the number of positive relative gene expression values and
n
is the number of non-zero values within each window.
For convenience, this function allows for the specification of multiple
window sizes using the span
argument. The result of a
movbin
call will generate a matrix with length(span)
rows
and length(v)
columns. Each row of the matrix represents the
data generated from each span. This matrix can be returned or the matrix
from can be condensed to a single vector of length v by
applying a summary function summarize
to the matrix columns.
Either a matrix or a vector containing the summarized z-scores from the applied binomial test.
Kyle A. Furge, Ph.D., kyle.furge@vai.org and Karl J. Dykema, karl.dykema@vai.org
x <- c(rnorm(50,mean=1),rnorm(50,mean=-1),rnorm(100)) layout(1:2) plot(x,type="h",ylim=c(-5,5)) ## apply the approximated binomial with a single span mb <- movbin(x,span=25,summarize=NULL) lines(mb[1,]) ## try a few different span ranges mb <- movbin(x,span=c(10,25,50),summarize=NULL) lines(mb[1,]) ## span of 10 lines(mb[2,]) ## span of 25 lines(mb[3,]) ## span of 50 ## average the results from the different spans plot(x,type="h",ylim=c(-5,5)) mb <- movbin(x,span=c(10,25,50),summarize=mean) lines(mb,col="blue") mb <- movbin(x,span=c(10,25,50),summarize=median) lines(mb,col="red")