preppi_download: Interactions from PrePPI

In saezlab/OmnipathR: OmniPath web service client and more

Interactions from PrePPI

Description

Retrieves predicted protein-protein interactions from the PrePPI database (http://honig.c2b2.columbia.edu/preppi). The interactions in this table are supposed to be correct with a > 0.5 probability.

Usage

preppi_download(...)

Arguments

...	Minimum values for the scores. The available scores are: str, protpep, str_max, red, ort, phy, coexp, go, total, exp and final. Furthermore, an operator can be passed, either .op = '&' or .op = '|', which is then used for combined filtering by multiple scores.

Details

PrePPI is a combination of many prediction methods, each resulting a score. For an explanation of the scores see https://honiglab.c2b2.columbia.edu/hfpd/help/Manual.html. The minimum, median and maximum values of the scores:

| Score   | Minimum | Median   | Maximum            |
| ------- | ------- | -------- | ------------------ |
| str     |       0 |     5.5  |           6,495    |
| protpep |       0 |     3.53 |          38,138    |
| str_max |       0 |    17.9  |          38,138    |
| red     |       0 |     1.25 |              24.4  |
| ort     |       0 |     0    |           5,000    |
| phy     |       0 |     2.42 |               2.42 |
| coexp   |       0 |     2.77 |              45.3  |
| go      |       0 |     5.86 |             181    |
| total   |       0 | 1,292    | 106,197,000,000    |
| exp     |       1 |   958    |           4,626    |
| final   |     600 | 1,778    |            4.91e14 |

Value

A data frame (tibble) of interactions with scores, databases and literature references.

See Also

preppi_filter

Examples

preppi <- preppi_download()
preppi
# # A tibble: 1,545,710 x 15
#    prot1 prot2 str_score protpep_score str_max_score red_score ort_score
#    <chr> <chr>     <dbl>         <dbl>         <dbl>     <dbl>     <dbl>
#  1 Q131. P146.     18.6           6.45         18.6      4.25      0.615
#  2 P064. Q96N.      1.83         14.3          14.3      4.25      0
#  3 Q7Z6. Q8NC.      4.57          0             4.57     0         0
#  4 P370. P154.    485.            0           485.       1.77      0.615
#  5 O004. Q9NR.     34.0           0            34.0      0.512     0
# # . with 1,545,700 more rows, and 8 more variables: phy_score <dbl>,
# #   coexp_score <dbl>, go_score <dbl>, total_score <dbl>, dbs <chr>,
# #   pubs <chr>, exp_score <dbl>, final_score <dbl>

saezlab/OmnipathR documentation built on Nov. 10, 2024, 11:02 p.m.