SEIR: Selector-Embedded Iterative Regression

In AlenLove/SEIRtest: Selector-Embedded Iterative Regression

Description

Selector-Embedded Iterative Regression

Usage

SEIR(
  Y,
  X,
  GM = NULL,
  CV = NULL,
  maxStep = 10,
  selector = c("L0", "L1", "MCP", "stepwise", "bess", "MARS", "SCAD", "lars", "vif",
    "SES", "FBED"),
  fun.selection = c("fastLm", "lm.vec"),
  extraction = c("bagging-like", "1se", "min", "mean"),
  X.check = c(TRUE, FALSE),
  chunk.num = NULL,
  file.output = TRUE,
  plot.style = "CMplot",
  cutOff = 0.05
)

Arguments

Y	Phenotypic vector with length n
X	n by m dataframe, matrix or big.matrix of genotype matrix
GM	m by 3 dataframe or matrix for SNP name, chromosome and BP
CV	n by t dataframe or matrix for t covariates
maxStep	maxStep Maximum number of iteration steps
selector	selector A method for Variable selection
fun.selection	fun.selection The core function for parameter calculation, lm.vec is more faster than fastLm
extraction	A method for calculating p values
X.check	logical
chunk.num	The "pieces" number of genotype matrix when considering memory size
file.output	output GWAS results, Manhattan and QQ plot
plot.style	plot.style
cutOff	The threshold

Value

List - includes the suggested SNPs, the results with normal 4-column format (SNP, chromosome, BP, p-values), the matrix of coefficients, SE, z-values, p-values, and the matrices of coefficients, SE, z-values, p-values from each iterative step

Examples

         data(geno)
         data(phe)
         data(map)
         SEIR(Y=phe,X=geno,GM=map,CV=NULL,maxStep=10,
              selector="stepwise",fun.selection="fastLm",
              extraction="min",X.check="FALSE",chunk.num = NULL,
              file.output=FALSE,plot.style="SEIR",cutOff=0.05)

AlenLove/SEIRtest documentation built on Dec. 17, 2021, 7:49 a.m.