genesFromRandomPathways: Function to randomly select genes associated with randomly...

Description Usage Arguments Value References See Also Examples

View source: R/genesFromRandomPathways.R

Description

This function first randomly selects a number (np) of pathways, then randomly selects a number (ng) of genes that are associated with at least one of the selected pathways. The function can be used to compare Sigora's performance to traditional overrepresentation tests.

Usage

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genesFromRandomPathways(seed = 1234, GPSrepo, np, ng)

Arguments

seed

A random seed.

GPSrepo

A signature repository (created by ..) or one of the precompiled options.

np

How many pathways to select.

ng

Number of genes to be selected.

Value

selectedPathways

A vector containing the "np" originally selected pathways.

genes

A vector containing the "ng" selected genes from selectedPathways.

References

Foroushani AB, Brinkman FS and Lynn DJ (2013).“Pathway-GPS and SIGORA: identifying relevant pathways based on the over-representation of their gene-pair signatures.”PeerJ, 1

See Also

sigora-package

Examples

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## select 50 genes from 3 human KEGG pathways
a1<-genesFromRandomPathways(seed=12345,kegH,3,50)
## originally selected pathways:
a1[["selectedPathways"]]
## what are the genes
a1[["genes"]]
## sigora's results
sigoraRes <- sigora(GPSrepo =kegH, queryList = a1[["genes"]],
        level = 4)
## compare to traditional methods results:
oraRes <- ora(a1[["genes"]],kegH)
dim(oraRes)
oraRes

Example output

### randomly selected pathways are: 
hsa04145 
 hsa05323 
 hsa00380 
[1] "hsa04145" "hsa05323" "hsa00380"
 [1] "ENSG00000090339" "ENSG00000204267" "ENSG00000167553" "ENSG00000019169"
 [5] "ENSG00000116039" "ENSG00000105953" "ENSG00000115008" "ENSG00000082781"
 [9] "ENSG00000117410" "ENSG00000137124" "ENSG00000150337" "ENSG00000242574"
[13] "ENSG00000170458" "ENSG00000007952" "ENSG00000108774" "ENSG00000102755"
[17] "ENSG00000164400" "ENSG00000250565" "ENSG00000258947" "ENSG00000102524"
[21] "ENSG00000153086" "ENSG00000196735" "ENSG00000237541" "ENSG00000241106"
[25] "ENSG00000116701" "ENSG00000159720" "ENSG00000135218" "ENSG00000143149"
[29] "ENSG00000259207" "ENSG00000005844" "ENSG00000078142" "ENSG00000227507"
[33] "ENSG00000150093" "ENSG00000241644" "ENSG00000121691" "ENSG00000162747"
[37] "ENSG00000167552" "ENSG00000109576" "ENSG00000178462" "ENSG00000164904"
[41] "ENSG00000104951" "ENSG00000115020" "ENSG00000185883" "ENSG00000152086"
[45] "ENSG00000113296" "ENSG00000106803" "ENSG00000119699" "ENSG00000112115"
[49] "ENSG00000111537" "ENSG00000197102"
   pathwy.id                           description   pvalues Bonferroni
6   hsa04145                             Phagosome 1.959e-33  5.485e-31
18  hsa05332             Graft-versus-host disease 8.288e-24  2.321e-21
11  hsa05130 Pathogenic Escherichia coli infection 1.827e-19  5.116e-17
2   hsa00380                 Tryptophan metabolism 3.736e-07  1.046e-04
12  hsa05145                         Toxoplasmosis 3.122e-05  8.742e-03
   successes PathwaySize      N sample.size
6      21.43      815.48 350891      116.03
18     15.00      612.25 350891      116.03
11     16.44     1529.91 350891      116.03
2       4.58      170.73 350891      116.03
12      9.37     4744.94 350891      116.03
[1] 29  7
      pathwyid                                                description
21215 hsa04966                             Collecting duct acid secretion
18308 hsa05310                                                     Asthma
4972  hsa05330                                        Allograft rejection
10482 hsa05332                                  Graft-versus-host disease
17452 hsa00380                                      Tryptophan metabolism
6942  hsa04940                                   Type I diabetes mellitus
10428 hsa04672               Intestinal immune network for IgA production
12316 hsa05144                                                    Malaria
17913 hsa00280                 Valine, leucine and isoleucine degradation
19585 hsa05110                                  Vibrio cholerae infection
17542 hsa05150                            Staphylococcus aureus infection
17491 hsa00310                                         Lysine degradation
5006  hsa05130                      Pathogenic Escherichia coli infection
18680 hsa05416                                          Viral myocarditis
10366 hsa05321                           Inflammatory bowel disease (IBD)
7727  hsa04721                                     Synaptic vesicle cycle
9643  hsa04612                        Antigen processing and presentation
17786 hsa05120 Epithelial cell signaling in Helicobacter pylori infection
11194 hsa05140                                              Leishmaniasis
12845 hsa05132                                       Salmonella infection
20378 hsa05322                               Systemic lupus erythematosus
12582 hsa04640                                 Hematopoietic cell lineage
19500 hsa05323                                       Rheumatoid arthritis
3509  hsa05145                                              Toxoplasmosis
19024 hsa04380                                 Osteoclast differentiation
6143  hsa04514                             Cell adhesion molecules (CAMs)
16694 hsa04145                                                  Phagosome
4809  hsa05164                                                Influenza A
20210 hsa05152                                               Tuberculosis
      success pathwaySize pvalues    Bonfer          NA
21215       4    hsa04966      27 4.626e-05 5.55120e-03
18308       4    hsa05310      27 4.626e-05 5.55120e-03
4972        5    hsa05330      34 4.964e-06 5.95680e-04
10482       6    hsa05332      36 2.372e-07 2.84640e-05
17452       9    hsa00380      39 7.336e-12 8.80320e-10
6942        6    hsa04940      40 4.567e-07 5.48040e-05
10428       5    hsa04672      44 1.830e-05 2.19600e-03
12316       6    hsa05144      45 9.416e-07 1.12992e-04
17913       4    hsa00280      46 3.866e-04 4.63920e-02
19585       6    hsa05110      50 1.785e-06 2.14200e-04
17542       8    hsa05150      50 2.699e-09 3.23880e-07
17491       5    hsa00310      51 3.802e-05 4.56240e-03
5006        7    hsa05130      53 1.151e-07 1.38120e-05
18680       6    hsa05416      55 3.163e-06 3.79560e-04
10366       8    hsa05321      62 1.586e-08 1.90320e-06
7727        5    hsa04721      63 1.062e-04 1.27440e-02
9643        6    hsa04612      65 8.506e-06 1.02072e-03
17786       5    hsa05120      68 1.530e-04 1.83600e-02
11194      11    hsa05140      68 1.761e-12 2.11320e-10
12845       5    hsa05132      84 4.136e-04 4.96320e-02
20378       7    hsa05322      84 2.826e-06 3.39120e-04
12582       6    hsa04640      85 4.012e-05 4.81440e-03
19500      19    hsa05323      85 3.680e-24 4.41600e-22
3509        7    hsa05145     111 1.813e-05 2.17560e-03
19024       7    hsa04380     125 3.925e-05 4.71000e-03
6143        7    hsa04514     139 7.744e-05 9.29280e-03
16694      31    hsa04145     147 5.853e-40 7.02360e-38
4809        7    hsa05164     163 2.103e-04 2.52360e-02
20210      15    hsa05152     168 7.503e-13 9.00360e-11

sigora documentation built on Aug. 24, 2019, 1:04 a.m.