p.exact: Exact p-values

In p.exact: Exact P-values for Genome-Wide Association Analyses in Inbred Populations

Description

p.exact: Exact P-values for Genome-Wide Association Analyses in Inbred Populations

Details

The p.exact package implements for calculating exact dataset-specific p-values for genome-wide association (GWA) analyses in inbred populations. The module is compatible with existing GenABEL/gwaa.data data formats.

For converting data from other formats, see

convert.snp.illumina (Illumina/Affymetrix-like format). convert.snp.text (conversion from human-readable GenABEL format), convert.snp.ped (Linkage, Merlin, Mach, and similar files), convert.snp.mach (Mach-format), convert.snp.tped (from PLINK TPED format), convert.snp.affymetrix (BRML-style files).

For converting of GenABEL's data to other formats, see export.merlin (MERLIN and MACH formats), export.impute (IMPUTE, SNPTEST and CHIAMO formats), export.plink (PLINK format, also exports phenotypic data).

To load the data, see load.gwaa.data.

For data managment and manipulations see merge.gwaa.data, merge.snp.data, gwaa.data-class, snp.data-class, snp.names, snp.subset.

Author(s)

Xia Shen

References

If you use p.exact package in your analysis, please cite the following work:

Xia Shen (2015). Beyond permutation test: calculating exact dataset-specific p-values for genome-wide association studies in inbred populations. Submitted.

See Also

GenABEL

p.exact documentation built on May 2, 2019, 6:10 p.m.