nice2x2Table: Checks for validity data representing an enrichment...

In pablof1988/goSorensen: Statistical inference based on the Sorensen-Dice dissimilarity and the Gene Ontology (GO)

Checks for validity data representing an enrichment contingency table generated from two gene lists

Description

Checks for validity data representing an enrichment contingency table generated from two gene lists

Usage

nice2x2Table(x)

## S3 method for class 'table'
nice2x2Table(x)

## S3 method for class 'matrix'
nice2x2Table(x)

## S3 method for class 'numeric'
nice2x2Table(x)

Arguments

x	either an object of class "table", "matrix" or "numeric".

Details

In the "table" and "matrix" interfaces, the input parameter x must correspond to a two-dimensional array:

n_{11}	n_{10}
n_{01}	n_{00},

These values are interpreted (always in this order) as n11: number of GO terms enriched in both lists, n01: GO terms enriched in the second list but not in the first one, n10: terms not enriched in the second list but enriched in the first one and double negatives, n00. The double negatives n00 are ignored in many computations concerning the Sorensen-Dice index.

In the "numeric" interface, the input x must correspond to a numeric of length 3 or more, in the same order as before.

Value

boolean, TRUE if x nicely represents a 2x2 contingency table interpretable as the cross-tabulation of the enriched GO terms in two gene lists: "Number of enriched terms in list 1 (TRUE, FALSE)" x "Number of enriched terms in list 2 (TRUE, FALSE)". In this function, "nicely representing a 2x2 contingency table" is interpreted in terms of computing the Sorensen-Dice dissimilarity and associated statistics. Otherwise the execution is interrupted.

Methods (by class)

• nice2x2Table(table): S3 method for class "table"

• nice2x2Table(matrix): S3 method for class "matrix"

• nice2x2Table(numeric): S3 method for class "numeric"

Examples

conti <- as.table(matrix(c(27, 36, 12, 501, 43, 15, 0, 0, 0), nrow = 3, ncol = 3,
                         dimnames = list(c("a1","a2","a3"),
                                         c("b1", "b2","b3"))))
tryCatch(nice2x2Table(conti), error = function(e) {return(e)})
conti2 <- conti[1,seq.int(1, min(2,ncol(conti))), drop = FALSE]
conti2
tryCatch(nice2x2Table(conti2), error = function(e) {return(e)})

conti3 <- matrix(c(12, 210), ncol = 2, nrow = 1)
conti3
tryCatch(nice2x2Table(conti3), error = function(e) {return(e)})

conti4 <- c(32, 21, 81, 1439)
nice2x2Table(conti4)
conti4.mat <- matrix(conti4, nrow = 2)
conti4.mat
conti5 <- c(32, 21, 81)
nice2x2Table(conti5)

conti6 <- c(-12, 21, 8)
tryCatch(nice2x2Table(conti6), error = function(e) {return(e)})

conti7 <- c(0, 0, 0, 32)
tryCatch(nice2x2Table(conti7), error = function(e) {return(e)})

pablof1988/goSorensen documentation built on Dec. 15, 2024, 12:01 p.m.