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count_by_maf()
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count number of loci below and above a maf threshold |
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fix_allele_encoding()
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Fixes allele encoding so that the minor allele homozygote is always encoded as 2 |
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get_effects()
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Get weights for markers using provided distribution function. |
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get_genotypes()
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Get genotypes matrix (counts of reference allele) from a GenABEL gwaa-data, vcfR object or
an object imported using seqminer |
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get_genotypes_gwaa_data()
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Get genotypes matrix (counts of reference allele) from a GenABEL gwaa-data object |
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get_genotypes_seqminer_matrix()
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Get genotypes matrix (counts of reference allele) from one of the seqminer
read functions that return genotype matrix |
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get_genotypes_vcfR()
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Get genotypes matrix (counts of reference allele) from a vcfR object |
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get_maf()
|
Get minor allele frequency vector |
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hush()
|
Silence too verbose code |
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impute_G()
|
Impute missing genotypes using minor allele frequency |
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plot_effects()
|
Plots effect sizes distribution dependent on minor allele frequency. |
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plot_mrk_density()
|
Plot density of markers in a region |
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read_region_vcf()
|
read specific region from VCF file to a gwasim type genotype matrix |
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read_regions_bed()
|
Read regions information from bed file. |
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recode_G()
|
Re-code genotypes according to the supplied genotype-phenotype map |
|
rnorm_betas()
|
Effect sizes $$ from a normal distribution. |
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scan_CommonRare()
|
Run SKAT-O CommonRare model on all regions |
|
sim_y_in_regions()
|
Simulate phenotypes in a number of regions |
|
simulate_phenotype() simulate_phenotype()
|
Simulate phenotype given a set of common and rare variants. |
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tibble_to_gwaa()
|
Convert tibble with genotypes along with a vector of phenotypes to GenABEL internal raw gwaa.data format. |
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tibble_to_raw_genotypes()
|
Convert tibble with genotypes to GenABEL internal raw genotype format and writ it into a file. |
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validate_maf()
|
Validate minor allele frequency vector |