ahp_weights: AHP weights slot

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

Description

ahp_weights is a slot of pipelineObj class. It consists of a list of matrices representing AHP priorities for all decision elements

Author(s)

Daryanaz Dargahi <[e-mail]>

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)
ahp_weights(result)

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.
$Prioritization_of_DE_genes
                        [,1]
Tumor_expression  0.46972977
Normal_expression 0.34067384
Frequency         0.11600194
Epitopes          0.07359445

$Tumor_expression
                 local      global
BSG|682     0.13057550 0.061335201
CD44|960    0.13057550 0.061335201
CD38|952    0.03643459 0.017114410
CA9|768     0.13057550 0.061335201
MUC16|94025 0.13057550 0.061335201
CD9|928     0.13057550 0.061335201
EGFR|1956   0.13057550 0.061335201
CD70|970    0.03643459 0.017114410
MUC1|4582   0.13057550 0.061335201
FZD10|11211 0.01310230 0.006154539

$Normal_expression
                 local     global
BSG|682     0.03665958 0.01248896
CD44|960    0.03665958 0.01248896
CD38|952    0.14247991 0.04853918
CA9|768     0.14247991 0.04853918
MUC16|94025 0.14247991 0.04853918
CD9|928     0.03665958 0.01248896
EGFR|1956   0.03665958 0.01248896
CD70|970    0.24678244 0.08407232
MUC1|4582   0.03665958 0.01248896
FZD10|11211 0.14247991 0.04853918

$Frequency
                 local      global
BSG|682     0.14470793 0.016786400
CD44|960    0.14470793 0.016786400
CD38|952    0.02138224 0.002480381
CA9|768     0.14470793 0.016786400
MUC16|94025 0.14470793 0.016786400
CD9|928     0.05876305 0.006816627
EGFR|1956   0.14470793 0.016786400
CD70|970    0.03022490 0.003506147
MUC1|4582   0.14470793 0.016786400
FZD10|11211 0.02138224 0.002480381

$Epitopes
                   local      global
Number_of_epitopes 0.125 0.009199304
Size_of_epitopes   0.875 0.064395151

$Number_of_epitopes
                 local       global
BSG|682     0.11111111 0.0010221449
CD44|960    0.11111111 0.0010221449
CD38|952    0.11111111 0.0010221449
CA9|768     0.11111111 0.0010221449
MUC16|94025 0.11111111 0.0010221449
CD9|928     0.05555556 0.0005110725
EGFR|1956   0.11111111 0.0010221449
CD70|970    0.11111111 0.0010221449
MUC1|4582   0.11111111 0.0010221449
FZD10|11211 0.05555556 0.0005110725

$Size_of_epitopes
            local      global
BSG|682       0.1 0.006439515
CD44|960      0.1 0.006439515
CD38|952      0.1 0.006439515
CA9|768       0.1 0.006439515
MUC16|94025   0.1 0.006439515
CD9|928       0.1 0.006439515
EGFR|1956     0.1 0.006439515
CD70|970      0.1 0.006439515
MUC1|4582     0.1 0.006439515
FZD10|11211   0.1 0.006439515

$Criteria_prioritization_matrix
            Tumor_expression Normal_expression   Frequency    Epitopes
BSG|682          0.061335201        0.01248896 0.016786400 0.007461660
CD44|960         0.061335201        0.01248896 0.016786400 0.007461660
CD38|952         0.017114410        0.04853918 0.002480381 0.007461660
CA9|768          0.061335201        0.04853918 0.016786400 0.007461660
MUC16|94025      0.061335201        0.04853918 0.016786400 0.007461660
CD9|928          0.061335201        0.01248896 0.006816627 0.006950588
EGFR|1956        0.061335201        0.01248896 0.016786400 0.007461660
CD70|970         0.017114410        0.08407232 0.003506147 0.007461660
MUC1|4582        0.061335201        0.01248896 0.016786400 0.007461660
FZD10|11211      0.006154539        0.04853918 0.002480381 0.006950588
            total_priorities
BSG|682           0.09807222
CD44|960          0.09807222
CD38|952          0.07559563
CA9|768           0.13412244
MUC16|94025       0.13412244
CD9|928           0.08759138
EGFR|1956         0.09807222
CD70|970          0.11215454
MUC1|4582         0.09807222
FZD10|11211       0.06412469

$Subcriteria_prioritization_matrix
            Tumor_expression Normal_expression   Frequency Number_of_epitopes
BSG|682          0.061335201        0.01248896 0.016786400       0.0010221449
CD44|960         0.061335201        0.01248896 0.016786400       0.0010221449
CD38|952         0.017114410        0.04853918 0.002480381       0.0010221449
CA9|768          0.061335201        0.04853918 0.016786400       0.0010221449
MUC16|94025      0.061335201        0.04853918 0.016786400       0.0010221449
CD9|928          0.061335201        0.01248896 0.006816627       0.0005110725
EGFR|1956        0.061335201        0.01248896 0.016786400       0.0010221449
CD70|970         0.017114410        0.08407232 0.003506147       0.0010221449
MUC1|4582        0.061335201        0.01248896 0.016786400       0.0010221449
FZD10|11211      0.006154539        0.04853918 0.002480381       0.0005110725
            Size_of_epitopes total_priorities
BSG|682          0.006439515       0.09807222
CD44|960         0.006439515       0.09807222
CD38|952         0.006439515       0.07559563
CA9|768          0.006439515       0.13412244
MUC16|94025      0.006439515       0.13412244
CD9|928          0.006439515       0.08759138
EGFR|1956        0.006439515       0.09807222
CD70|970         0.006439515       0.11215454
MUC1|4582        0.006439515       0.09807222
FZD10|11211      0.006439515       0.06412469

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