KW.hit.express {GRIN2} | R Documentation |
Associate Lesion Groups with Gene Expression
Description
Performs the Kruskal Wallis (KW) test to evaluate the association between lesion groups and the expression level of the corresponding gene.
Usage
KW.hit.express(alex.data, gene.annotation, min.grp.size = NULL)
Arguments
alex.data |
Output from the
|
gene.annotation |
Gene annotation table. Must be a |
min.grp.size |
Minimum number of patients required in a lesion group to be included in the test. For a gene to be tested, there must be at least two groups with more than |
Details
For each row in the row.mtch
table, the function performs a Kruskal Wallis test comparing expression values of the gene across lesion groups.
The lesion groups are defined in the alex.lsn
matrix. Patients with multiple types of lesions in a gene are assigned the label "multiple"
,
and those with no lesion are labeled "none"
. The expression values are obtained from the corresponding row in alex.expr
.
The function tests whether expression levels significantly differ across lesion groups for the same gene.
Value
A data frame where each row corresponds to a gene tested. Columns include:
gene |
Ensembl gene ID. |
gene.name |
HGNC gene symbol. |
p.KW |
Kruskal Wallis test p-value. |
q.KW |
FDR-adjusted q-value for multiple testing correction. |
_n.subjects |
Number of subjects in each lesion group, including "none" and "multiple". |
_mean |
Mean expression per lesion group. |
_median |
Median expression per lesion group. |
_sd |
Standard deviation of expression per lesion group. |
Author(s)
Abdelrahman Elsayed abdelrahman.elsayed@stjude.org and Stanley Pounds stanley.pounds@stjude.org
References
Hollander, M., & Wolfe, D. A. (1973). Nonparametric Statistical Methods. New York: Wiley. pp. 115-120.
Cao, X., Elsayed, A. H., & Pounds, S. B. (2023). Statistical Methods Inspired by Challenges in Pediatric Cancer Multi-omics.
See Also
Examples
data(expr_data)
data(lesion_data)
data(hg38_gene_annotation)
# Prepare matched lesion-expression data
alex.data <- alex.prep.lsn.expr(expr_data, lesion_data,
hg38_gene_annotation,
min.expr = 1, min.pts.lsn = 5)
# Perform Kruskal Wallis test between lesion groups and expression levels:
alex.kw.results <- KW.hit.express(alex.data,
hg38_gene_annotation,
min.grp.size = 5)