Main function of the RVPedigree package
1 2 3 
method 
character, selects the method to use for the association testing. Can be one of the following:

y 
vector of phenotype data (one entry per individual), of length n. 
X 
matrix of covariates including intercept (dimension: n \times p, with p the number of covariates) 
Phi 
Relationship matrix (i.e. twice the kinship matrix); an n \times n square symmetric positivedefinite matrix. 
filename 
character, path to input file containing haplotype data 
type 
character, 
regions 
a data frame with details of the genomic regions in
which the association test specified by the
Any other columns will be ignored. 
weights 
optional numeric vector of genotype weights. If
this option is not specified, the beta distribution is used
for weighting the variants, with each weight given by
w_i = dbeta(f_i, 1, 25)^2, with f_i the minor
allele frequency (MAF) of variant i. This default is the
same as used by the

Nperm 
(integer) The number of permutations to be done to calculate the empirical pvalue if the VCC2 or VCC3 method is used. For other methods this parameter is ignored (default: 100). 
pvalThreshold 
(numeric) Threshold for the association pvalue. Regions with a pvalue below this threshold will not be present in the output data frame (default: 0.1). 
VCC3afterVCC1 
(logical) Boolean value that indicates
whether the VCC3 method should automatically be run on the
variants passing the pvalue threshold set using the

Ncores 
(integer) Number of processor (CPU) cores to be used in parallel when doing running the association analysis. If the number of regions is larger than the number of cores, then each region gets to use maximum one core. If the number of cores is larger than the number of regions and the VCC2 or VCC3 methods are selected, the remaining cores are distributed among the regions to parallelize the permutations used to determine the pvalue (default: 1). 
The RVPedigree function is the main function of the RVPedigree used package.
Under the hood this function calls ASKAT.region
,
NormalizedASKAT.region
,
VCC1.region
, VCC2.region
or
VCC3.region
, depending on the method
parameter specified by the user.
A data frame containing results of the association test
specified by the method
parameter for each region in
the data frame specified by the regions
parameter. The
output data frame contains the following columns:
Score.Test
: the score of the given association test
P.value
: the pvalue of the association test
N.Markers
: the number of markers in the region
regionname
: Name of the regions/genes on which you
are running the association tests
Note that regions that do not contain any genetic variants will be removed from the output.
Lennart C. Karssen
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