kimma_cleaning: kmFit data cleaning

In BIGslu/kimma: Kinship In Mixed Model Analysis of RNA-seq

kmFit data cleaning

Description

Data

Usage

kimma_cleaning(
  dat = NULL,
  kin = NULL,
  patientID = "ptID",
  libraryID = "libID",
  counts = NULL,
  meta = NULL,
  genes = NULL,
  weights = NULL,
  subset_var = NULL,
  subset_lvl = NULL,
  subset_genes = NULL,
  model_lm = NULL,
  genotype_name = NULL,
  run_lmerel = FALSE
)

Arguments

dat	EList object output by voom( ). Contains counts (dat$E), meta (dat$targets), and genes (dat$genes).
kin	Matrix with pairwise kinship values between individuals. Must be numeric with rownames.
patientID	Character of variable name to match dat$targets to kinship row and column names.
libraryID	Character of variable name to match dat$targets to dat$E colnames Alternate data if not using EList object
counts	Matrix of normalized expression. Rows are genes, columns are libraries.
meta	Matrix or data frame of sample and individual metadata.
genes	Matrix or data frame of gene metadata.
weights	Matrix or data frame of gene specific weights Subset data (optional)
subset_var	Character list of variable name(s) to filter data by.
subset_lvl	Character list of variable value(s) or level(s) to filter data to. Must match order of subset_var
subset_genes	Character vector of genes to include in models.
model_lm	Character vector of simple linear model version of model provided
genotype_name	Character string. Used internally for kmFit_eQTL

Value

Data frame formatted for use in kmFit

BIGslu/kimma documentation built on May 30, 2024, 10:09 p.m.