genesPulmonDB: Homogenized values of PulmonDB

In AnaBVA/PulmonDB: Package to download data from PulmonDB

Description

This gives you a S3 object with homogenized values and annotation per contrast.

Usage

genesPulmonDB(gene, id)

Arguments

gene	A value or character vector with gene names. It also accepts 'all' for downloading every available gene.
id	A value or character vector with GSEs (GEO id).

Details

Homogenized values are contrasts of a sample reference vs a test reference in log2. We have performed normalization using RMA for Affymetrix platform and loess normalization for non-Affymetrix.

Rownames are genes (e.i."MMP7","JUND") and colnames are contrasts (GSMXX1.ch1-vs-GSMXX2.ch1) in which the first GSM (GSMXX1.ch1) is the test and the second GSM (GSMXXX2.ch1) is the reference. The annotation follows annotationPulmonDB() output, and has the same order.

Examples

a <- genesPulmonDB(c("MMP1","JUND"), c("GSE1122","GSE101286"))
## annotation
#colData(a)
## values
#assays(a)$values
#assay(a)
#All genes
all_genes <- genesPulmonDB("all","GSE1122")
#Value of MMP7
gse <- c("GSE32537","GSE21369","GSE24206","GSE94060","GSE72073","GSE35145","GSE52453")
mmp7 <- genesPulmonDB("MMP7",gse)


## Not run: 
## a comment
genesPulmonDB("MMP1","JUND", c("GSE1122"))

## End(Not run)

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