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
GO:0003954_NADH dehydrogenase activity	molecular_function
GO:0005739_mitochondrion	cellular_component
GO:0005747_mitochondrial respiratory chain complex I	cellular_component
GO:0006120_mitochondrial electron transport, NADH to ubiquinone	biological_process
GO:0008137_NADH dehydrogenase (ubiquinone) activity	molecular_function
GO:0016021_integral 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

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