Description Usage Arguments Value Author(s) Examples
Function SPIATest
computes SPIA distance and performs probabilistic test
on a set of cell lines.
1 2 3 4 |
x |
a matrix with a column for each cell line and a row for each SNP |
row.names |
specify if the first column of x contains SNPs names/identificators |
test.prob |
specify if the function has to perform SPIA probabilistic test |
test.param |
specify the parameters of the probabilistic test.
|
verbose |
print verbose information |
SPIAresult |
a matric with a line for each cell line and with columns with the informationss about distances In particular, each row of SPIAresult has 7 columns:
|
parameters |
the parameters used by the test (test.param) |
input.param |
the number of samples (N_samples), the number of SNPs (N_SNPs), and if the probabilistic test has been done (test.prob) |
Francesca Demichelis <francesca.demichelis@unitn.it>, Davide Prandi <davide.prandi@unitn.it>
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 | library(SPIAssay)
# An example of genotype calls with:
# - four cell lines
# - for each cell line five SNP calls
GenotypeCalls <- rbind(
c("SNP1", "AA", "AA", "AB", "AB"),
c("SNP2", "NoCall", "AA", "AB", "AB"),
c("SNP3", "AB", "AB", "AA" , "AB"),
c("SNP4", "BB", "BB", "BB", "BB"),
c("SNP5", "AB", "BB", "AA", "AA"))
colnames(GenotypeCalls) <-
c("SNP_ID","CellLine1","CellLine2","CellLine3","CellLine4")
# Encode the data into SPIA format.
# SPIA uses 0 for AA, 1 for BB, 2 for AB, and NA for NoCall
# therefore, GenotypeCalls has to be encoded by meand of
# toSPIAData
encoding <- c("AA","BB","AB","NoCall")
SPIAGenotypeCalls <- toSPIAData(GenotypeCalls,encoding)
# Perform SPIA analysis
SPIAanalysis <- SPIATest(SPIAGenotypeCalls)
# This analysis give an error because there are not enough SNPs
# Perform SPIA analysis with parameters SPIAParam
# to reduce the 'similar' region
SPIAParam <-
list(Pmm=0.1, nsigma=1, Pmm_nonM=0.6, nsigma_nonM=1, PercValidCall=0.7)
SPIAanalysis <-
SPIATest(SPIAGenotypeCalls,row.names=TRUE,test.prob=TRUE,SPIAParam)
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