API for rqtl/qtl2scan
Genome Scans for QTL Experiments

Global functions
Rcpp_calcLL Source code
Rcpp_calc_logdetXpX Source code
Rcpp_eigen_decomp Source code
Rcpp_eigen_rotation Source code
Rcpp_fitLMM Source code
Rcpp_fitLMM_mat Source code
Xgenocol_to_snpcol Source code
Xgenoprob_to_snpprob Source code
align_scan1_map Source code
alleleprob_to_snpprob Source code
batch_cols Man page Source code
batch_vec Source code
bayes_int Man page Source code
bayes_int_plain Source code
c.scan1perm Man page
calc_coefSE_binreg Source code
calc_coefSE_binreg_eigenqr Source code
calc_coefSE_binreg_weighted Source code
calc_coefSE_binreg_weighted_eigenqr Source code
calc_coefSE_linreg Source code
calc_coefSE_linreg_eigenchol Source code
calc_coefSE_linreg_eigenqr Source code
calc_coef_binreg Source code
calc_coef_binreg_eigenqr Source code
calc_coef_binreg_weighted Source code
calc_coef_binreg_weighted_eigenqr Source code
calc_coef_linreg Source code
calc_coef_linreg_eigenchol Source code
calc_coef_linreg_eigenqr Source code
calc_fitted_linreg_eigenchol Source code
calc_fitted_linreg_eigenqr Source code
calc_hsq_clean Source code
calc_ll_binreg Source code
calc_ll_binreg_eigenchol Source code
calc_ll_binreg_eigenqr Source code
calc_ll_binreg_weighted Source code
calc_ll_binreg_weighted_eigenchol Source code
calc_ll_binreg_weighted_eigenqr Source code
calc_mvrss_eigenchol Source code
calc_mvrss_eigenqr Source code
calc_resid_eigenchol Source code
calc_resid_eigenqr Source code
calc_resid_linreg Source code
calc_resid_linreg_3d Source code
calc_rss_eigenchol Source code
calc_rss_eigenqr Source code
calc_rss_linreg Source code
calc_sdp Man page Source code Source code
cbind.scan1 Man page Source code
cbind.scan1perm Man page Source code
cbind_expand Source code
check4names Source code
check_binary_pheno Source code
check_extra_dots Source code
check_kinship Source code
check_kinship_onechr Source code
chr_lengths Man page Source code
cluster_lapply Source code
collapse_chr_lengths_to_AX Source code
colnames4attr Source code
decomp_kinship Man page Source code
dim.calc_genoprob Source code
dimnames.calc_genoprob Source code
double_kinship Source code
drop_depcols Source code
drop_xcovar Source code
est_herit Man page Source code
expand_genoprobs_intcovar Source code
expand_interval_to_markers Source code
find_intervals Source code
find_lin_indep_cols Source code
find_matching_cols Source code
find_peaks Man page Source code Source code
find_peaks_and_bayesint Source code Source code
find_peaks_and_lodint Source code Source code
fit1 Man page Source code
fit1_binary_addcovar Source code
fit1_binary_intcovar Source code
fit1_hk_addcovar Source code
fit1_hk_intcovar Source code
fit1_pg Source code
fit1_pg_addcovar Source code
fit1_pg_intcovar Source code
fit_binreg Source code
fit_binreg_eigenqr Source code
fit_binreg_weighted Source code
fit_binreg_weighted_eigenqr Source code
fit_linreg Source code
fit_linreg_eigenchol Source code
fit_linreg_eigenqr Source code
force_intcovar Source code
formX_intcovar Source code
gen_strat_perm Source code
genocol_to_snpcol Source code
genoprob_to_snpprob Man page Source code Source code
genoprobs_by_contrasts Source code
genoprobs_col2drop Source code
get_common_ids Man page Source code
get_permutation Source code
grab_dots Source code
hsq_dimnames Source code
index_batches_by_omits Source code
index_snps Man page Source code
interp_map Man page Source code
interpolate_map Source code
invert_sdp Man page Source code
is_cluster Source code
is_kinship_decomposed Source code
is_kinship_list Source code
is_same Source code
isnt_karl Source code
lod_int Man page Source code
lod_int_plain Source code
map2chr Source code
map2markernames Source code
map2pos Source code
mat2strata Man page Source code
matrix_x_3darray Source code
matrix_x_matrix Source code
matrix_x_vector Source code
max.scan1 Man page Source code
max_scan1 Man page Source code
maxlod Man page Source code
n_cores Source code
null_binary_clean Source code
nullrss_clean Source code
nvert_sdp Source code
permute_ivector Source code
permute_ivector_stratified Source code
permute_nvector Source code
permute_nvector_stratified Source code
pick_marker_subset Man page Source code Source code
print.summary.scan1perm Man page Source code
qtl2scan Man page
qtl2scan-package Man page
random_int Source code
rbind.scan1 Man page Source code
rbind.scan1perm Man page Source code
rev_snp_index Source code
scan1 Man page Source code
scan1_binary_clean Source code
scan1_clean Source code
scan1_pg Source code
scan1_pg_clean Source code
scan1blup Man page Source code
scan1blup_pg Source code
scan1coef Man page Source code
scan1coef_names Source code
scan1coef_pg Source code
scan1perm Man page Source code
scan1perm_covar Source code
scan1perm_nocovar Source code
scan1perm_pg Source code
scan1perm_pg_onechr Source code
scan1snps Man page Source code
scan1snps_snpinfo Source code
scan_binary_onechr Source code
scan_binary_onechr_intcovar_highmem Source code
scan_binary_onechr_intcovar_lowmem Source code
scan_binary_onechr_intcovar_weighted_highmem Source code
scan_binary_onechr_intcovar_weighted_lowmem Source code
scan_binary_onechr_weighted Source code
scan_hk_onechr Source code
scan_hk_onechr_intcovar_highmem Source code
scan_hk_onechr_intcovar_lowmem Source code
scan_hk_onechr_intcovar_weighted_highmem Source code
scan_hk_onechr_intcovar_weighted_lowmem Source code
scan_hk_onechr_nocovar Source code
scan_hk_onechr_weighted Source code
scan_pg_onechr Source code
scan_pg_onechr_intcovar_highmem Source code
scan_pg_onechr_intcovar_lowmem Source code
scanblup Source code
scancoefSE_binary_addcovar Source code
scancoefSE_binary_intcovar Source code
scancoefSE_hk_addcovar Source code
scancoefSE_hk_intcovar Source code
scancoefSE_pg_addcovar Source code
scancoefSE_pg_intcovar Source code
scancoef_binary_addcovar Source code
scancoef_binary_intcovar Source code
scancoef_hk_addcovar Source code
scancoef_hk_intcovar Source code
scancoef_pg_addcovar Source code
scancoef_pg_intcovar Source code
setup_cluster Source code
snpinfo_to_map Source code
sqrt_weights Source code
subset.calc_genoprob Source code
subset.scan1 Man page
subset_chr Source code
subset_ind Source code
subset_kinship Source code
subset_scan1 Man page Source code
summary.scan1perm Man page Source code
summary_scan1perm Man page Source code
top_snps Man page Source code
weighted_3darray Source code
weighted_matrix Source code
rqtl/qtl2scan documentation built on Feb. 3, 2018, 2:53 p.m.