Description Usage Arguments Value Author(s) See Also Examples
View source: R/get.scores.pvalues.R
For each tested SNP and each parameter in the model, computes scores by summing family scores over all families and computes the corresponding p-values. P-values of global and joint tests are also computed.
1 | get.scores.pvalues(test, joint.tests)
|
test |
object returned by |
joint.tests |
list of vectors of numbers between 1 and the total number of parameters in the |
data frame of p-values for all the tested SNPs, for the global test (all parameters tested jointly), the individual tests and other joint tests specified by the argument joint.tests
. The p-values are obtained from scores summed over all families. These scores of individual tests are also included in this data frame.
Alexandre Bureau and Jordie Croteau
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 | data(fat2Lpoly.allSNPs)
joint.tests=list(c(2,5),c(3,4))
get.scores.pvalues(fat2Lpoly.allSNPs, joint.tests)
# snp.cond snp.test global_p params.joint_2-5_p params.joint_3-4_p param_1_score
# 1 snp4.loc1 snp2.loc2 5.80e-03 7.12e-01 0.000954 0.449
# 2 snp4.loc1 snp4.loc2 2.14e-07 1.24e-05 0.000954 0.449
# 3 snp4.loc1 snp5.loc2 1.14e-03 1.44e-01 0.000954 0.449
# 4 snp4.loc1 snp6.loc2 5.59e-04 3.84e-02 0.000954 0.449
# 5 snp4.loc1 snp8.loc2 1.15e-03 1.55e-01 0.000954 0.449
# param_2_score param_3_score param_4_score param_5_score param_1_p param_2_p
# 0.333 -1.427 3.638 0.733 0.653 0.739
# 0.890 -1.427 3.638 4.612 0.653 0.373
# 0.776 -1.427 3.638 1.785 0.653 0.438
# -0.082 -1.427 3.638 2.553 0.653 0.934
# 0.869 -1.427 3.638 1.695 0.653 0.385
# param_3_p param_4_p param_5_p
# 1 0.154 0.000275 0.464000
# 2 0.154 0.000275 0.000004
# 3 0.154 0.000275 0.074200
# 4 0.154 0.000275 0.010700
# 5 0.154 0.000275 0.090100
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