Description Usage Arguments Details Value Author(s)
genoAssoc
takes genotype data in GenABEL gwaa
format and performs association analysis.
1 2 3 4 5 6 7 8 9 10 11 12 |
gwaa |
|
projectfolder |
character containing path to output folder (will be generated if not existing). |
projectname |
character used as suffix for output files. |
trait.name |
character indicating trait(s) of interest. |
trait.type |
character with data type of analysed trait. Either "gaussian", "binomial" or "guess" (latter option guesses trait type). |
fun.assoc |
character with association function from GenABEL package to be used.
Either |
gtmode |
character with mode of inheritance if regression is used.
Either |
times |
If more than one, the number of permutations to be used for calculationg empirical p-values. Relevant for score test only. |
quiet |
logical Do not print warning messages. |
TopHitsReported |
numeric with number of top hits to report. Use nsnps(gwaa.object) for all SNPs. |
GenABEL package is used for association analysis of a gwaa
object.
The trait of interest is given in trait.name
either as single trait (e.g. affection
)
or as formula (e.g. affection01 ~ Age + sex
) if association shall be adjusted for covariates.
All traitnames in trait.name
must exist within the phenotype data of the gwaa
object.
Use phdata(gwaa)
for checking which trait names are avalable.
Either linear or logistic regression or fast score test can be used for association as given in fun.assoc
.
In case of regression, the mode of inheritance is given in gtmode
.
If the fast score test from GenABELs qtscore
-function is used without covariates, the function is equivalent
to Armitage TREND Test. If covariates are used, the trait is analysed using GLM
.
Set times
to more than 1, to calculate empirical p-values for the score test using times
permutations.
A table and a Manhattan plot with association results are stored in projectfolder
.
scan.gwaa
object with Association results. Intermediary results and plots are stored
in projectfolder
as side effects.
Frank Ruehle
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