ProsCan_Length: The Prostate Cancer Data Example: Gene Length Information

In gu-mi/GOglm: Length Bias Correction in Gene Ontology Enrichment Analysis Using Logistic Regression

Description

Similar to ProsCan_DE, we include in this dataset each gene's length to be passed as the second argument to the prepare function.

Details

A gene's length is defined as the median length of all its corresponding mature transcripts. In the goseq package, length data are obtained from the UCSC genome browser for each combination of genome and id. In GOglm, we assume that end-users already have the length information available, so that a column of gene lengths is properly matched to the gene names (row names) in the data frame. For an illustration on accessing gene length information, please see the Example section of goglm.

Source

http://www.ncbi.nlm.nih.gov/pubmed/19088194

References

Mi G, Di Y, Emerson S, Cumbie JS and Chang JH (2012) "Length bias correction in Gene Ontology enrichment analysis using logistic regression", PLOS ONE, 7(10): e46128.

Li H, Lovci M, Kwon Y, Rosenfeld M, Fu X, et al. (2008) "Determination of tag density required for digital transcriptome analysis: application to an androgen-sensitive prostate cancer model", Proc Natl Acad Sci U S A 105: 20179-20184.

Young M, Wakefield M, Smyth G, Oshlack A (2010) "Gene ontology analysis for RNA-seq: accounting for selection bias", Genome Biol 11: R14.

Robinson M, McCarthy D, Smyth G (2010) "edgeR: a Bioconductor package for differential expression analysis of digital gene expression data", Bioinformatics 26: 139-140.

Examples

## Load the dataset into R session:
data(ProsCan_Length)
Length_data <- ProsCan_Length

## Another dataset from this package:
data(ProsCan_DE)
DE_data <- ProsCan_DE

## Prepare a data frame to be passed to goglm():
gene_table <- prepare(DE_data, Length_data, trans.p = "d.log", trans.l = TRUE)
## Check first 10 rows of the data frame:
gene_table[1:10,1:2]

## We can call the summary() function:
summary(gene_table)

## We can also call the plot() function:
plot(gene_table)

gu-mi/GOglm documentation built on May 14, 2019, 7:42 a.m.