README.md

In hdzierz/rkaka: R API to Database Kaka (rkaka)

R API for Kaka

Tools

• R/knitr
• KAKA's restful API
• Jupyter notebooks in form of a Pyrat

R

The R API is very similar to PyKaka. It loads data from the database Kaka using its RESTful API.

Kaka runs using docker. The docker installation includes a Pyrat (Jupyter notebook) instance on port 8888. rkaka is pre-installed on that pyrat instance.

Installation

If you are on the above mentioned Kaka Pyrat instance just call library("rkaka"). Otherwise use:

devtools::install_github("hdzierz/rkaka")

Use it

The syntax for the API is as follows:

kaka.qry(realm='some_realm', qry='some_query') 

Whereby:

"realm" can currrently be:

• genotype
• kiwifruit

"qry":

This is a pql query. For more info see: pql

"mode":

• pql (default)
• mongo (can perform better for larger queries)

Return value:

The return value is an R data frame.

Example:

To obtain data from Kaka you run which loads an example data set:

dat <- kaka.qry('genotype', experiment=='Gene Expression')
dat

Or more complicated:

dat <- kaka.qry('genotype', "experiment=='Gene Expression' and gene==regex('^AT1G029.*')")
dat

Gene expression data (any data really) can be supplemented with exprimental design information similar to the old micro array targets file:

dat <- kaka.qry('design', "experiment=='Gene Expression'")
dat

    phenotype   condition   typ
1   PFD1001L3R1 treated paired-end
2   PFD1001L3R2 treated paired-end
3   PFD1001L4R1 treated paired-end
4   PFD1001L4R2 treated paired-end
5   PFD1002L3R1 untreated   paired-end
6   PFD1002L3R2 untreated   paired-end
7   PFD1002L4R1 untreated   paired-end
8   PFD1002L4R2 untreated   paired-end

DESeq2

pathview

hdzierz/rkaka documentation built on May 17, 2019, 3:19 p.m.