pipeline: pipeline

In Prize: Prize: an R package for prioritization estimation based on analytic hierarchy process

Description

a pipeline for prioritization estimation using analytic hierarchy process (AHP), which supports both relative and rating AHP models.

Usage

pipeline(srcfile, model, simulation = 500)

Arguments

srcfile	a character matrix, where the first column specifies the hierarchy order, the second column includes elements IDs, and the third column includes the path to the PCM/priority matrices (See the example below).
model	the AHP computation model. Choose from relative and rating models. If using the relative model pairwise comparison matrices must be provided for the evaluation of alternatives. However, if using the raing model, rating matrices must be provided for the evaluation of alternatives.
simulation	simulation size for computation of Saaty's inconsistency

Value

An S4 object including the ahp wight and consistancy measures, and data structures to visualize with ahplot(), rainbowplot(), and wplot().

Author(s)

Daryanaz Dargahi

Examples

mat <- matrix(nrow = 7, ncol = 3, data = NA)
mat[,1] <- c('0', '1','2','3','4','4.1','4.2')
mat[,2] <- c('Prioritization_of_DE_genes','Tumor_expression','Normal_expression',
             'Frequency', 'Epitopes', 'Number_of_epitopes', 'Size_of_epitopes')
mat[,3] <- c(system.file('extdata','aggreg.judgement.tsv',package = 'Prize'),
             system.file('extdata','tumor.PCM.tsv',package = 'Prize'),
             system.file('extdata','normal.PCM.tsv',package = 'Prize'),
             system.file('extdata','freq.PCM.tsv',package = 'Prize'),
             system.file('extdata','epitope.PCM.tsv',package = 'Prize'),
             system.file('extdata','epitopeNum.PCM.tsv',package = 'Prize'),
             system.file('extdata','epitopeLength.PCM.tsv',package = 'Prize'))

result <- pipeline(mat, model = 'relative', simulation = 500)

Example output

0 Prioritization_of_DE_genes is processed.
1 Tumor_expression is processed.
2 Normal_expression is processed.
3 Frequency is processed.
4 Epitopes is processed.
4.1 Number_of_epitopes is processed.
4.2 Size_of_epitopes is processed.

Prize documentation built on April 28, 2020, 7:48 p.m.