alex.waterfall.prep: Prepare Lesion and Expression Data for Waterfall Plots

In GRIN2: Genomic Random Interval (GRIN)

Prepare Lesion and Expression Data for Waterfall Plots

Description

Function prepares lesion and expression data of a selected gene for the alex.waterfall.plot function.

Usage

alex.waterfall.prep(alex.data, alex.kw.results, gene, lsn.data)

Arguments

alex.data	output of the alex.prep.lsn.expr function. It's a list of three data tables that include "row.mtch", "alex.expr" with expression data, "alex.lsn" with lesion data. Rows of alex.expr, and "alex.lsn" matrices are ordered by the gene ensembl IDs and columns are ordered by patient IDs.
alex.kw.results	ALEX Kruskal-Wallis test results (output of the KW.hit.express function).
gene	Gene name or ensembl ID of the gene of interest.
lsn.data	Lesion data in a GRIN compatible format. Object should has five columns that include "ID" with patient ID, "chrom" which is the chromosome on which the lesion is located, "loc.start" which is the lesion start position, "loc.end" the lesion end position and "lsn.type" which is the lesion category for example gain, loss, mutation, fusion, etc...

Details

Function prepares lesion and expression data of a selected gene for the alex.waterfall.plot function. It return a data table with patient ID, lesion types that affect each patient if any and expression level of the gene of interest. It also extract the kruskal-wallis test result and all lesions that affect the gene of interest.

Value

A list of four components:

gene.lsn.exp	Data table with three columns("ID" with patient ID, "gene.name_lsn" has the type of lesion affecting the patient which can be none, gain, mutation, multiple, etc.. and "gene.name_expr" which has the expression level of the gene of interst in this particular patient.
lsns	Data table with all lesions affecting the gene of interst in a GRIN compatible format extracted from the lesion data file.
stats	One row with the Kruskal-Wallis test result for the gene of interst (output of the KW.hit.express function).
gene.ID	Gene name of the gene of interst.

Author(s)

Abdelrahman Elsayed [e-mail] and Stanley Pounds [e-mail]

References

Cao, X., Elsayed, A. H., & Pounds, S. B. (2023). Statistical Methods Inspired by Challenges in Pediatric Cancer Multi-omics.

See Also

alex.prep.lsn.expr(), KW.hit.express()

Examples

data(expr.data)
data(lesion.data)
data(hg19.gene.annotation)

# prepare expression, lesion data and return the set of genes with both types of data available
# ordered by gene IDs in rows and patient IDs in columns:
alex.data=alex.prep.lsn.expr(expr.data, lesion.data,
                             hg19.gene.annotation, min.expr=1, min.pts.lsn=5)

# run KW test for association between lesion groups and expression level of the same gene:
alex.kw.results=KW.hit.express(alex.data, hg19.gene.annotation, min.grp.size=5)

# To prepare lesion and expression data for a waterfall plot (WT1 gene):
WT1.waterfall.prep=alex.waterfall.prep(alex.data, alex.kw.results, "WT1", lesion.data)

GRIN2 documentation built on April 4, 2025, 1:41 a.m.