DMRforPairs (version 1.8.0)

calc_stats: CALCULATE DESCRIPTIVE AND TEST STATISTICS

Description

Calculate the (difference in) median beta and M values for the rows specified in probe_rows (descriptive statistics). probe_rows must specify a continuous range of adjacent probes. If a regions shows an high difference (>dM_min) between any pair of samples, the differences are formally tested (Mann Whitney U if n=2, Kruskal Wallis n>2). If n>2 and the omnibus test is significant , pairwise testing is performed to determine which differ significantly.

Usage

calc_stats(probe_rows,probes,m,b,n,dMth,do.format=FALSE)

Arguments

probe_rows

Vector of row numbers in regions$valid.m, regions$valid.beta or regions$perprobe identifying adjacent probes. See output regionfinder

probes

see output of regionfinder (regions$perprobe)

m

see output of regionfinder (regions$valid.m)

b

see output of regionfinder (regions$valid.beta)

n

total number of samples

dMth

see min_dM parameter of DMRforPairs

do.format

see testregion

Value

Data frame or vector with statistics and test results concerning the probes specified in probe_rows (please see description).

Details

The p-values reported by this function are not yet adjusted for multiple testing. This function is rarely called by the user directly.

See Also

DMRforPairs, regionfinder, testregion.

Examples

#calc_stats() is an integrated part of the DMRforPairs() wrapper and is 
#not usually called by the user directly. Please see DMRforPairs() for 
#an example.