CrossSpeciesCombat: A function for merging expression data from human and mouse...

In syspremed/PanNETassigner: A cross-species analysis in pancreatic neuroendocrine tumors reveals molecular subtypes with distinctive clinical, metastatic, developmental, and metabolic characteristics.

Description

Combat is used to remove batch effect and merge two expression datasets from two species, human and mouse.

Usage

CrossSpeciesCombat(human, mouse, ordered)

Arguments

human	is human.data dataset which contains the PanNET core clinical mRNA expression data.
mouse	is mouse.data dataset which contains mouse RT2 mRNA expression data
ordered	is the ordered samples across species.

Details

This function selects the most variable genes (standard deviation greater than 0.8) in both datasets. Combat is used to remove batch effect and merge two gene expression datasets from different species.

Value

The output of this function is the merged human and mouse expression data saved in your working directory under PanNetResults/CrossSpeciesCombat folder.

Author(s)

Anguraj Sadanandam [e-mail]

References

Anguraj Sadanandam, et all (2015). A cross-species analysis in pancreatic neuroendocrine tumors reveals molecular subtypes with distinctive clinical, metastatic, developmental, and metabolic characteristics. Accepted.

Examples

## Three datasets are required for this function 
data(human.data)
data(mouse.data)
data(CrossSpeciesCombat.ordered)
## Run the function
CrossSpeciesCombat(human.data,mouse.data,CrossSpeciesCombat.ordered)

syspremed/PanNETassigner documentation built on May 31, 2019, 12:48 a.m.