basal: Basal dataset: A composition of cancer datasets with top...

In hheiling/glmmPen: High Dimensional Penalized Generalized Linear Mixed Models (pGLMM)

Basal dataset: A composition of cancer datasets with top scoring pairs (TSPs) as covariates and binary response indicating if the subject's cancer subtype was basal-like. A dataset composed of four datasets combined from studies that contain gene expression data from subjects with several types of cancer. Two of these datasets contain gene expression data for subjects with Pancreatic Ductal Adenocarcinoma (PDAC), one dataset contains data for subjects with Breast Cancer, and the fourth dataset contains data for subjects with Bladder Cancer. The response of interest is whether or not the subject's cancer subtype was the basal-like subtype. See articles Rashid et al. (2020) "Modeling Between-Study Heterogeneity for Improved Replicability in Gene Signature Selection and Clinical Prediction" and Moffitt et al. (2015) "Virtual microdissection identifies distinct tumor- and stroma-specific subtypes of pancreatic ductal adenocarcinoma" for further details on these four datasets.

Description

Basal dataset: A composition of cancer datasets with top scoring pairs (TSPs) as covariates and binary response indicating if the subject's cancer subtype was basal-like.

A dataset composed of four datasets combined from studies that contain gene expression data from subjects with several types of cancer. Two of these datasets contain gene expression data for subjects with Pancreatic Ductal Adenocarcinoma (PDAC), one dataset contains data for subjects with Breast Cancer, and the fourth dataset contains data for subjects with Bladder Cancer. The response of interest is whether or not the subject's cancer subtype was the basal-like subtype. See articles Rashid et al. (2020) "Modeling Between-Study Heterogeneity for Improved Replicability in Gene Signature Selection and Clinical Prediction" and Moffitt et al. (2015) "Virtual microdissection identifies distinct tumor- and stroma-specific subtypes of pancreatic ductal adenocarcinoma" for further details on these four datasets.

Usage

data("basal")

Format

A list containing the following elements:

y

binary response vector; 1 indicates that the subject's cancer was of the basal-like subtype, 0 otherwise

X

matrix of 50 top scoring pair (TSP) covariates

group

factor indicating which cancer study the observation belongs to, which are given the following descriptions: UNC PDAC, TCGA PDAC, TCGA Bladder Cancer, and UNC Breast Cancer

Z

model matrix for random effects; organized first by variable, then by group (i.e. by cancer study)

hheiling/glmmPen documentation built on Jan. 15, 2024, 11:47 p.m.