View source: R/KW.hit.express.R
KW.hit.express | R Documentation |
Performs the Kruskal Wallis (KW) test to evaluate the association between lesion groups and the expression level of the corresponding gene.
KW.hit.express(alex.data, gene.annotation, min.grp.size = NULL)
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 |
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.
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. |
Abdelrahman Elsayed abdelrahman.elsayed@stjude.org and Stanley Pounds stanley.pounds@stjude.org
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.
alex.prep.lsn.expr
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)
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