alex.prep.lsn.expr: Prepare Lesion and Expression Data for Kruskal-Wallis Test

In GRIN2: Genomic Random Interval (GRIN)

Prepare Lesion and Expression Data for Kruskal-Wallis Test

Description

The function prepares lesion and expression data matrices for the KW.hit.express function that runs the kruskal-Wallis test for the association between lesion groups and expression level of each gene with available lesion and expression data.

Usage

alex.prep.lsn.expr(
  expr.mtx,
  lsn.data,
  gene.annotation,
  min.expr = NULL,
  min.pts.lsn = NULL
)

Arguments

expr.mtx	Normalized log2 transformed expression data provided by the user with genes in rows and subjects in columns (first column "ensembl.ID" should be gene ensembl IDs).
lsn.data	Lesion data in GRIN compatible format. Data frame 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 type for example gain, loss, mutation, fusion, etc...
gene.annotation	Gene annotation data either provided by the user or retrieved from ensembl BioMart database using get.ensembl.annotation function included in the GRIN2.0 library. Data.frame should has four columns: "gene" which is the ensembl ID of annotated genes, "chrom" which is the chromosome on which the gene is located, "loc.start" which is the gene start position, and "loc.end" the gene end position.
min.expr	Minimum allowed expression level of the gene (the sum of expression level of the gene in all patients; useful to exclude genes with very low expression)
min.pts.lsn	Minimum number of patients with any type of lesions in a certain gene otherwise the gene will be excluded from the lesion matrix.

Details

The function use prep.lsn.type.matrix function to prepare the lesion matrix that has each gene represented in one row with all lesion types included. Next, the function will prepare lesion and expression data matrices for the KW.hit.express function that runs the kruskal-Wallis test. It only keep genes with both lesion and expression data with rows ordered by ensembl ID and columns ordered by patient's ID.

Value

A list with the following components:

alex.expr	Expression data with gene ensembl IDs as row names and patient IDs as column names. Rows are ordered by ensembl ID and columns ordered by patient IDs.
alex.lsn	Lesion data for genes in the expression data matrix with gene ensembl IDs as row names and patient IDs as column names. Rows are ordered by ensembl ID and columns ordered by patient IDs.
alex.row.mtch	Data.frame of two columns with ensembl ID of genes in the expression and lesion data matrices (ID should be the same in the two columns).

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

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)

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