README.md

In luciorq/aaegdata: Aedes aegypti Mosquitoes Molecular Information

aaegdata

This is a data package containing Aedes aegypti vector mosquitoes biologically relevant molecular and biochemical data. Data colected from public available databases and presented here in a clean, structured and ready to use format. The consistent format used for the data allows the use of modern syntax and tools to be used with this package.

Installation

You can install the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("luciorq/aaegdata")

Examples

Those are basic examples which shows you how to solve common problems:

Check first 15 genes that changed annotation in AaegL5.1

library(dplyr)
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union

aaegdata::annotation_conversion %>%
  dplyr::filter( !is.na(gene_aaegl35) & !is.na(gene_aaegl51)) %>%
  dplyr::filter( gene_aaegl35 != gene_aaegl51 ) %>%
  head(15)

| gene_aaegl35 | gene_aaegl51 | |:--------------|:--------------| | AAEL000003 | AAEL021256 | | AAEL000014 | AAEL019508 | | AAEL000015 | AAEL019624 | | AAEL000015 | AAEL019625 | | AAEL000034 | AAEL023601 | | AAEL000054 | AAEL021963 | | AAEL000060 | AAEL024813 | | AAEL000062 | AAEL022948 | | AAEL000067 | AAEL026496 | | AAEL000068 | AAEL021083 | | AAEL000070 | AAEL021708 | | AAEL000082 | AAEL020708 | | AAEL000083 | AAEL019508 | | AAEL000086 | AAEL026937 | | AAEL000093 | AAEL025818 |

Retrieving gene ontologies for a gene

## Using gene AAEL000986
aaegdata::go_gene_sets %>%
  dplyr::filter(gene == "AAEL000986") %>%
  dplyr::select( -gene)

| gene_ontology | go_domain | |:------------------------------------------------------------------|:--------------------| | dehydrogenase activity | molecular_function | | | cellular_component | | respiratory chain complex I | cellular_component | | electron transport, NADH to ubiquinone | biological_process | | dehydrogenase (ubiquinone) activity | molecular_function | | component of membrane | cellular_component |

Checking gene description by part of name

library(stringr)
aaegdata::gene_description %>%
  dplyr::filter( stringr::str_detect( gene_name, "Rpl") )

| gene | description | gene_name | |:-----------|:----------------------------------------------------------------------------|:-----------| | AAEL000010 | 60S ribosomal protein L36 [Source:UniProtKB/TrEMBL;Acc:Q1HR17] | Rpl36-1 | | AAEL000823 | 60S ribosomal protein L35A, putative [Source:UniProtKB/TrEMBL;Acc:Q17N60] | Rpl35 | | AAEL002639 | 60S ribosomal protein L36 [Source:UniProtKB/TrEMBL;Acc:Q17HK5] | Rpl36-2 |

Computed homology in the closest model organism (D. melanogaster)

aaegdata::aaeg_dmel_orthologs %>%
  dplyr::filter( gene == "AAEL000986")

| gene | dmel_gene | dmel_gene_name | dmel_homology_type | dmel_to_aaeg_identity| aaeg_to_dmel_identity| dmel_protein | |:-----------|:------------|:-----------------|:---------------------|-------------------------:|-------------------------:|:--------------| | AAEL000986 | FBgn0029888 | ND-ASHI | ortholog_one2one | 56.3218| 56| FBpp0070950 |

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

luciorq/aaegdata documentation built on May 27, 2019, 11:49 p.m.