ccfast {GenABEL} | R Documentation |
Fast case-control analysis by computing chi-square test from 2x2 (allelic) or 2x3 (genotypic) tables
ccfast(y, data, snpsubset, idsubset, times=1, quiet=FALSE,bcast=10,clambda=TRUE,propPs=1.0)
y |
character name of the vector of case-control status. Cases are denoted as 1 and controls as 0. |
data |
An object of gwaa.data-class |
snpsubset |
Index, character or logical vector with subset of SNPs to run analysis on.
If missing, all SNPs from data are used for analysis. |
idsubset |
Index, character or logical vector with subset of IDs to run analysis on.
If missing, all people from data are used for analysis. |
times |
If more then one, the number of replicas to be used in derivation of
empirical genome-wide significance. See emp.qtscore , which
calls qtscore with times>1 for details |
quiet |
do not print warning messages |
bcast |
If the argument times > 1, progress is reported once in bcast replicas |
clambda |
If inflation facot Lambda is estimated as lower then one, this parameter controls if the original P1df (clambda=TRUE) to be reported in Pc1df, or the original 1df statistics is to be multiplied onto this "deflation" factor (clambda=FALSE). If a numeric value is provided, it is used as a correction factor. |
propPs |
proportion of non-corrected P-values used to estimate the inflation factor Lambda,
passed directly to the estlambda |
Object of class scan.gwaa-class
Yurii Aulchenko
emp.ccfast
,
plot.scan.gwaa
,
scan.gwaa-class
data(srdta) a <- ccfast("bt",data=srdta,snps=c(1:10),ids=c(1:100)) a a <- ccfast("bt",data=srdta) plot(a)