gSAME: Association analysis using gene-level association analysis.
In Sun-lab/SAME: Somatic mutation Association test with Measurement Errors

View source: R/gSAME.R

gSAME

R Documentation

Association analysis using gene-level association analysis.

Description

Association analysis using gene-level association analysis.

Usage

gSAME(Y, X, O, D, A, out_type = "C", theta_init, d0 = 20, null = FALSE,
  sig = NULL, spesen = NULL, mix_2bb = NULL, mix_4bb = NULL,
  min_altcount = 1, maxIt = 200, converged = 1e-06, reEst = 1,
  traceIt = 0, ...)

Arguments

`Y`	The response variable. Could be continuous or binary.
`X`	The design matrix. Intercept included.
`O`	A matrix for the observed somatic mutation.
`D`	A matrix for the total read-depth.
`A`	A matrix for the number of alternative number matrix.
`out_type`	The outcome type, "C" for continous, "D" for dichotomous. Default is "C".
`theta_init`	The initail values of the parameters. Can be NULL.
`d0`	The minimum of the total read-depth for obtaining the observed somatic mutation value. The default value is 20.
`null`	Logical. Indicating the estimation using EM algorim under the null hypothesis or not. The default is FALSE.
`sig`	A matrix with the likelihood of O, D, A conditioning on the true value of the somatic mutation (S=0/1) for all the samples. Default is NULL.
`spesen`	A dataframe specifying the specificity and sensitivity for all the somatic mutations.
`mix_2bb`	A dataframe indicating the parameters of two beta-binomial distributions depending on the true value of the somatic mutation when the read-depth is low.
`mix_4bb`	A dataframe indicating the parameters of four beta-binomial distributions depending on the values of the observed somatic mutaton and the true somatic mutation when the read-depth is high.
`min_altcount`	The mimimum of the number of alternative reads that the somatic mutation could acutally orrur. The default value is 1.
`converged`	The tolerance for the convergence. Default is 1e-6.
`mix_4bb`	A dataframe indicating the parameters of four beta-binomial distributions depending on the values of the observed somatic mutaton and the true somatic mutation when the read-depth is high.
`maxIT`	The maximal number of the EM iteration times. Default is 200.