DEET (version 1.0.11)

DEET_feature_extract: DEET_feature_extract

Description

Identify which genes are associated with pieces of metadata that a researcher queries.

Usage

DEET_feature_extract(mat, response, datatype, detection_cutoff = 0.7)

Value

Named list given the elastic net coefficients and the eleastic net regression between the response variable and the DEGs within DEET. It also outputs the correlation, ANOVA, and wilcoxon test of every gene against the response variable based on if it's continuous, categorical, or binomial in nature.

• elastic_net_coefficients - Association that a gene has with the response variable based on the elastic net regression.

• elastic_net - Output of the elastic net regression

• - basic_features gives the output of the correlation, ANOVA, and wilcoxon test of every gene against the response variable.

Arguments

mat

A gene-by-study matrix populated by the coefficients of that study. By default, the coefficient is the log2Fold-change of genes as long as they are differentially expressed (cutoff = padj < 0.05).

response

A vector (binomial, categorical, or continuous) that is used to associated the DEGs within the studies.

datatype

indication of whether the response variable is binomial, categorical, or continuous.

detection_cutoff

Proportion of studies where the gene is detected (not as DE but detected at all, designated with a FC != 0). Default value 0.7.

Author

Dustin Sokolowski, Jedid Ahn

References

Engebretsen, S., & Bohlin, J. (2019). Statistical predictions with glmnet. Clinical epigenetics, 11(1), 1-3.

Examples

data(DEET_feature_extract_example_matrix)
data(DEET_feature_extract_example_response)
single1 <- DEET_feature_extract(DEET_feature_extract_example_matrix,
DEET_feature_extract_example_response,"categorical")