annotationPulmonDB: Annotation from PulmonDB

In AnaBVA/PulmonDB: Package to download data from PulmonDB

Description

This gives you manually curated annotation for all GSEs available in PulmonDB.

Usage

annotationPulmonDB(id, output = "contrast")

Arguments

id	A value or character vector with GSEs (GEO id).
output	"contrast" or "sample". Default is "contrast" but it also can be changed to return annotation per "sample"

Details

Details. PulmonDB has contrast values (test_condition vs reference), which curated annotation can be returned using annotationPulmonDB(), default option is annotation by "contrast" and it will give you a string with the test and the reference annotation separated by "_vs_" (EMPHYSEMA_vs_HEALTHY/CONTROL).

It also has the opption to retrieve annotation per sample using the condition output = "sample".

Sometimes the feature annotated can be empty when two o more GSEs are downloaded. Each GSE has different annotation and not allways all annotation features are available.

Value

This is the result.

Source

http://pulmondb.liigh.unam.mx/

See Also

[genesPulmonDB()]

Examples

## Annotation per contrast
annotationPulmonDB("GSE27536")
annotationPulmonDB("GSE27536","contrast")
## Annotation per sample
annotationPulmonDB(c("GSE101286","GSE1122"),"sample")

AnaBVA/PulmonDB documentation built on Nov. 21, 2020, 7:35 p.m.