run_analysis: Run differential splicing anaysis.

In ruolin/raspberry: Differential spliced transcripts analysis based on multinomial logistic regression

Description

Run differential splicing anaysis.

Usage

run_analysis(dataDir, cases, MAX_ITER = 8, BIAS = F,
  FPKM_filter = 0.1, MCMC = FALSE, verbose = FALSE)

Arguments

dataDir	A string for the path of the input data dir.
cases	A vector of strings indicating which samples are treatment samples.
MAX_ITER	A number for the max iteration num for the EM algorithm. Default is 8.
BIAS	A boolean for doing bias correction or not, default is False
FPKM_filter	A number for fpkm filtering. Default is 1.0.
MCMC	A boolean for using MCMC instead of EM algorithm for optimization. Note that this will be very slow. Default is False.
verbose	A boolean for more verbose messages. Default is False.

Value

A list of genes. Each gene has multiple data.frame

Examples

run_analysis("my_path_to_data", c("caseSample1, caseSample2, caseSample3"), MAX_ITER = 5, BIAS = F, FPKM_filter = 1.0, MCMC = FALSE, verbose = FALSE)

ruolin/raspberry documentation built on Jan. 1, 2020, 8:39 a.m.