runAllMirnaModels: runAllMirnaModels runModel for all miRNAs

In Mercedeh66/mirTarRnaSeq: mirTarRnaSeq

runAllMirnaModels runModel for all miRNAs

Description

This function runs the "runModel" function for all miRNAs and mRNA combinations of two and returns a list with significant genes and FDR models

Usage

runAllMirnaModels(
  mirnas,
  DiffExpmRNA,
  DiffExpmiRNA,
  miranda_data,
  prob = 0.75,
  fdr_cutoff = 0.1,
  method = "fdr",
  cutoff = 0.05,
  all_coeff = FALSE,
  mode = NULL,
  family = glm_poisson(),
  scale = 1
)

Arguments

mirnas	vector of unique miRNAs under investigation.
DiffExpmRNA	deferentially/expressed mRNAs expression file.
DiffExpmiRNA	deferentially/expressed miRNAs expression file.
miranda_data	getInputSpecies output file ( use low filters).
prob	user defined ratio for miRanda distribution for miRanda score selection default is 0.75.
fdr_cutoff	cutoff for FDR selection default is 0.1.
method	finInterResult miRNA and mRNA interrelation in two time points results in a dataframe.
cutoff	P-value cutoff of the model.
all_coeff	if true only models with all negative coefficients will be selected if false at least one negative coefficient should be in the model; default is TRUE.
mode	model mode, default is Null, can be changed to "multi" and "inter".
family	Default is glm_poisson(), for zero inflated negative binomial NB option use glm_zeroinfl(dist="negbin").
scale	if normalized data (FPKM,RPKM,TPM,CPM), scale to 10 etc., however the higher you go on #scale the less accuracy your p-value estimate will be.

Value

List of run models

Examples

mirnas <- c("ebv-mir-bart9-5p", "ebv-mir-bart6-3p")
x <- runAllMirnaModels(mirnas, mRNA, miRNA, miRanda,
    prob = 0.90, fdr_cutoff = 0.1, method = "fdr",
    all_coeff = TRUE, mode = "multi",
    family = glm_poisson(), scale = 100
)

Mercedeh66/mirTarRnaSeq documentation built on April 14, 2023, 6:49 a.m.