equivSummary: This function returns a brief summary of the equivalence test...

In goProfiles: goProfiles: an R package for the statistical analysis of functional profiles

Description

Function to return a brief summary of the equivalence test between two profiles. If In its current version it is better that equivalentGOProfiles is called with option simplify set to FALSE before equivSummary can be used

Usage

equivSummary(l, decs = 6)

Arguments

l	A list of comparison results as returned by a call to compareGenelists
decs	Number of decimal places to use in the output

Value

A data frame with the summarized results of each comparison. The values contained are: Sqr.Eucl.Dist: The squared euclidean distance, Standard Err: The standard error estimate, pValue p value of the equivalence test, up conf.intUpper value for the desired condfidence interval. d0Threshold value for equivalence test. Equivalent?Numerical value set to 1 if profiles can be considered equivalent and to zero if they cannot.

Author(s)

Alex Sanchez

See Also

'equivalentGOProfiles'

Examples

# data(prostateIds)
# expandedWelsh <- expandedProfile(welsh01EntrezIDs[1:100], onto="MF",
#                        level=2, orgPackage="org.Hs.eg.db")
# expandedSingh <- expandedProfile(singh01EntrezIDs[1:100], onto="MF",
#                        level=2, orgPackage="org.Hs.eg.db")
#commonGenes <- intersect(welsh01EntrezIDs[1:100], singh01EntrezIDs[1:100])
#commonExpanded <- expandedProfile(commonGenes, onto="MF", level=2, orgPackage="org.Hs.eg.db")

# equivMF <-equivalentGOProfiles (pn=expandedWelsh, 
#                          qm  = expandedSingh, 
#                          pqn0= commonExpanded)
#print(equivSummary(equivMF, decs=5))

goProfiles documentation built on Nov. 8, 2020, 8:12 p.m.