ora: Traditional Overrepresentation Analysis.

Description Usage Arguments Details Value See Also Examples

View source: R/ora.R

Description

Traditional Overrepresentation Analysis by hypergeometric test: pathways are treated as collections of individual genes and all genes are treated as equally informative. This function is provided for comparison of the results of traditional methods to Sigora.

Usage

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ora(geneList, GPSrepo, idmap=sigora::idmap)

Arguments

geneList

A vector containing the list of genes of interest (e.g. differentially expressed genes). Following Identifier types are supported: Gene Symbols, ENTREZ-IDs or ENSEMBL-IDs.

GPSrepo

A GPS-repository (either one of the provided precomputed GPS repositories) or one created by makeGPS.

idmap

A dataframe for converting between different gene-identifier types (e.g. ENSEMBL, ENTREZ and HGNC-Symbols of genes). Most users do not need to set this argument, as there is a built-in conversion table.

Details

The primary purpose of makeGPS is to create a GPS repository. It does, however, retain the original "single gene"-"pathway" associations for the purpose of followup analyses, such as comparison of sigora-results to traditional methods. ora is an implementation of the traditional (individual gene) Overrepresentation Analysis.

Value

A dataframe with individual gene ORA results.

See Also

sigora-package

Examples

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data(kegM)
## select 50 genes from 3 mouse pathways
a1<-genesFromRandomPathways(seed=345,kegM,3,50)
## originally selected pathways:
a1[["selectedPathways"]]
## compare to traditional methods results:
oraRes <- ora(a1[["genes"]],kegM)
dim(oraRes)
oraRes

Example output

### randomly selected pathways are: 
mmu00790 
 mmu01524 
 mmu04072 
[1] "mmu00790" "mmu01524" "mmu04072"
[1] 88  6
   pathwyid                                              description success
1  mmu04072                        Phospholipase D signaling pathway      36
2  mmu04015                                   Rap1 signaling pathway      19
3  mmu05231                             Choline metabolism in cancer      15
4  mmu01522                                     Endocrine resistance      14
5  mmu01524                                 Platinum drug resistance      13
6  mmu01521                EGFR tyrosine kinase inhibitor resistance      13
7  mmu04540                                             Gap junction      13
8  mmu05215                                          Prostate cancer      13
9  mmu04915                               Estrogen signaling pathway      14
10 mmu05214                                                   Glioma      11
11 mmu05218                                                 Melanoma      11
12 mmu04923                    Regulation of lipolysis in adipocytes      10
13 mmu04210                                                Apoptosis      13
14 mmu04213          Longevity regulating pathway - multiple species      10
15 mmu04151                               PI3K-Akt signaling pathway      18
16 mmu04664                          Fc epsilon RI signaling pathway      10
17 mmu04071                           Sphingolipid signaling pathway      12
18 mmu04062                              Chemokine signaling pathway      14
19 mmu05161                                              Hepatitis B      12
20 mmu04725                                      Cholinergic synapse      11
21 mmu04014                                    Ras signaling pathway      14
22 mmu05230                      Central carbon metabolism in cancer       9
23 mmu04211                             Longevity regulating pathway      10
24 mmu04912                                   GnRH signaling pathway      10
25 mmu04024                                   cAMP signaling pathway      13
26 mmu04510                                           Focal adhesion      13
27 mmu04370                                   VEGF signaling pathway       8
28 mmu05213                                       Endometrial cancer       8
29 mmu05210                                        Colorectal cancer       9
30 mmu04722                           Neurotrophin signaling pathway      10
31 mmu04914                  Progesterone-mediated oocyte maturation       9
32 mmu04611                                      Platelet activation      10
33 mmu05223                               Non-small cell lung cancer       8
34 mmu04917                              Prolactin signaling pathway       8
35 mmu04371                                 Apelin signaling pathway      10
36 mmu04910                                Insulin signaling pathway      10
37 mmu05220                                 Chronic myeloid leukemia       8
38 mmu05166                                         HTLV-I infection      13
39 mmu04261                   Adrenergic signaling in cardiomyocytes      10
40 mmu04012                                   ErbB signaling pathway       8
41 mmu04022                               cGMP-PKG signaling pathway      10
42 mmu05167        Kaposi's sarcoma-associated herpesvirus infection      11
43 mmu04140                                       Autophagy - animal       9
44 mmu04068                                   FoxO signaling pathway       9
45 mmu04916                                            Melanogenesis       8
46 mmu05211                                     Renal cell carcinoma       7
47 mmu04660                        T cell receptor signaling pathway       8
48 mmu05142                Chagas disease (American trypanosomiasis)       8
49 mmu05221                                   Acute myeloid leukemia       7
50 mmu04662                        B cell receptor signaling pathway       7
51 mmu05224                                            Breast cancer       9
52 mmu05145                                            Toxoplasmosis       8
53 mmu00790                                      Folate biosynthesis       5
54 mmu04150                                   mTOR signaling pathway       9
55 mmu04921                               Oxytocin signaling pathway       9
56 mmu04919                        Thyroid hormone signaling pathway       8
57 mmu04650                Natural killer cell mediated cytotoxicity       8
58 mmu04630                               Jak-STAT signaling pathway       9
59 mmu04810                         Regulation of actin cytoskeleton      10
60 mmu04666                         Fc gamma R-mediated phagocytosis       7
61 mmu04913                                  Ovarian steroidogenesis       6
62 mmu05222                                   Small cell lung cancer       7
63 mmu04010                                   MAPK signaling pathway      11
64 mmu04720                                   Long-term potentiation       6
65 mmu04066                                  HIF-1 signaling pathway       7
66 mmu04932                Non-alcoholic fatty liver disease (NAFLD)       8
67 mmu04976                                           Bile secretion       6
68 mmu05205                                  Proteoglycans in cancer       9
69 mmu04724                                    Glutamatergic synapse       7
70 mmu05164                                              Influenza A       8
71 mmu04750         Inflammatory mediator regulation of TRP channels       7
72 mmu04270                       Vascular smooth muscle contraction       7
73 mmu05160                                              Hepatitis C       7
74 mmu04020                                Calcium signaling pathway       8
75 mmu04550 Signaling pathways regulating pluripotency of stem cells       7
76 mmu05418                   Fluid shear stress and atherosclerosis       7
77 mmu04620                     Toll-like receptor signaling pathway       6
78 mmu04933     AGE-RAGE signaling pathway in diabetic complications       6
79 mmu04215                             Apoptosis - multiple species       4
80 mmu04931                                       Insulin resistance       6
81 mmu04668                                    TNF signaling pathway       6
82 mmu04960                Aldosterone-regulated sodium reabsorption       4
83 mmu04918                                Thyroid hormone synthesis       5
84 mmu04971                                   Gastric acid secretion       5
85 mmu05212                                        Pancreatic cancer       5
86 mmu04970                                       Salivary secretion       5
87 mmu04973                    Carbohydrate digestion and absorption       4
88 mmu04152                                   AMPK signaling pathway       6
   pathwaySize   pvalues       Bonfer
1          147 2.509e-51 4.290390e-49
2          209 5.719e-17 9.779490e-15
3           99 8.415e-17 1.438965e-14
4           93 1.148e-15 1.963080e-13
5           77 2.883e-15 4.929930e-13
6           80 4.871e-15 8.329410e-13
7           86 1.306e-14 2.233260e-12
8           97 6.624e-14 1.132704e-11
9          133 1.951e-13 3.336210e-11
10          71 1.349e-12 2.306790e-10
11          72 1.584e-12 2.708640e-10
12          55 2.912e-12 4.979520e-10
13         136 5.667e-12 9.690570e-10
14          62 1.032e-11 1.764720e-09
15         358 1.382e-11 2.363220e-09
16          68 2.705e-11 4.625550e-09
17         122 2.965e-11 5.070150e-09
18         199 5.069e-11 8.667990e-09
19         143 1.951e-10 3.336210e-08
20         113 2.468e-10 4.220280e-08
21         233 4.186e-10 7.158060e-08
22          64 4.444e-10 7.599240e-08
23          90 4.746e-10 8.115660e-08
24          90 4.746e-10 8.115660e-08
25         197 6.234e-10 1.066014e-07
26         199 7.067e-10 1.208457e-07
27          58 5.300e-09 9.063000e-07
28          58 5.300e-09 9.063000e-07
29          88 8.121e-09 1.388691e-06
30         121 8.925e-09 1.526175e-06
31          90 9.933e-09 1.698543e-06
32         124 1.133e-08 1.937430e-06
33          66 1.522e-08 2.602620e-06
34          72 3.071e-08 5.251410e-06
35         139 3.419e-08 5.846490e-06
36         140 3.663e-08 6.263730e-06
37          76 4.736e-08 8.098560e-06
38         282 4.879e-08 8.343090e-06
39         147 5.845e-08 9.994950e-06
40          84 1.049e-07 1.793790e-05
41         168 2.071e-07 3.541410e-05
42         217 2.411e-07 4.122810e-05
43         130 2.505e-07 4.283550e-05
44         132 2.856e-07 4.883760e-05
45         100 4.111e-07 7.029810e-05
46          68 4.124e-07 7.052040e-05
47         101 4.441e-07 7.594110e-05
48         101 4.441e-07 7.594110e-05
49          69 4.565e-07 7.806150e-05
50          72 6.133e-07 1.048743e-04
51         147 7.151e-07 1.222821e-04
52         108 7.450e-07 1.273950e-04
53          26 8.669e-07 1.482399e-04
54         153 1.003e-06 1.715130e-04
55         153 1.003e-06 1.715130e-04
56         115 1.206e-06 2.062260e-04
57         118 1.467e-06 2.508570e-04
58         165 1.890e-06 3.231900e-04
59         215 2.024e-06 3.461040e-04
60          87 2.244e-06 3.837240e-04
61          57 2.602e-06 4.449420e-04
62          92 3.275e-06 5.600250e-04
63         294 4.877e-06 8.339670e-04
64          67 6.781e-06 1.159551e-03
65         105 7.934e-06 1.356714e-03
66         151 9.330e-06 1.595430e-03
67          71 9.525e-06 1.628775e-03
68         204 1.082e-05 1.850220e-03
69         114 1.366e-05 2.335860e-03
70         168 2.039e-05 3.486690e-03
71         125 2.496e-05 4.268160e-03
72         129 3.062e-05 5.236020e-03
73         134 3.914e-05 6.692940e-03
74         184 3.931e-05 6.722010e-03
75         137 4.512e-05 7.715520e-03
76         143 5.937e-05 1.015227e-02
77          99 6.410e-05 1.096110e-02
78         100 6.783e-05 1.159893e-02
79          32 7.002e-05 1.197342e-02
80         109 1.098e-04 1.877580e-02
81         110 1.155e-04 1.975050e-02
82          38 1.393e-04 2.382030e-02
83          73 1.540e-04 2.633400e-02
84          74 1.643e-04 2.809530e-02
85          75 1.751e-04 2.994210e-02
86          78 2.108e-04 3.604680e-02
87          43 2.269e-04 3.879990e-02
88         126 2.437e-04 4.167270e-02

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