API for rqtl/qtl2
Quantitative Trait Locus Mapping in Experimental Crosses

Global functions
.Xgenoprob_to_snpprob Source code
.alleleprob_to_snpprob Source code
.bayes_int_plain Source code
.calc_errorlod Source code
.calc_genoprob Source code
.calc_genoprob2 Source code
.calc_kinship Source code
.calc_sdp Source code
.check_crossinfo Source code
.check_is_female_vector Source code
.chisq_colpairs Source code
.clean_genoprob Source code
.compare_geno Source code
.count_invalid_genotypes Source code
.count_xo Source code
.count_xo_3d Source code
.crosstype_supported Source code
.est_map Source code
.est_map2 Source code
.find_ibd_segments Source code
.find_peaks Source code
.find_peaks_and_bayesint Source code
.find_peaks_and_lodint Source code
.genoprob_to_alleleprob Source code
.genoprob_to_snpprob Source code
.get_x_covar Source code
.guess_phase_A Source code
.guess_phase_X Source code
.guess_phase_f2A Source code
.guess_phase_f2X Source code
.interp_genoprob_onechr Source code
.invert_sdp Source code
.is_phase_known Source code
.locate_xo Source code
.lod_int_plain Source code
.maxmarg Source code
.predict_snpgeno Source code
.reduce_markers Source code
.sim_geno Source code
.sim_geno2 Source code
.viterbi Source code
.viterbi2 Source code
CCaltcolors Man page
CCcolors Man page
CCorigcolors Man page
Rcpp_calcLL Source code
Rcpp_calcLL_mat 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
[.calc_genoprob Man page
[.cross2 Man page
[.sim_geno Man page
[.viterbi Man page
`[.calc_genoprob` Source code
`[.cross2` Source code
`[.sim_geno` Source code
`[.viterbi` Source code
add_lod_labels Source code
add_threshold Man page Source code
addgenorect Source code
addlog Source code
align_geno_sex_cross Source code
align_scan1_map Man page Source code
any_duplicates Source code
arrange_genes Source code
assign_allele_codes Source code
basic_summaries Man page
batch_cols Man page Source code
batch_vec Man page Source code
bayes_int Man page 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_entropy Man page Source code
calc_errorlod Man page Source code
calc_fitted_linreg_eigenchol Source code
calc_fitted_linreg_eigenqr Source code
calc_geno_freq Man page Source code
calc_genoprob Man page Source code
calc_genoprob2 Source code
calc_grid Man page Source code
calc_grid_onechr Source code
calc_het Man page Source code
calc_hsq_clean Source code
calc_kinship Man page Source code
calc_kinship_bychr Source code
calc_kinship_overall 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_nullLL_clean Source code
calc_raw_founder_maf Man page Source code
calc_raw_geno_freq Man page Source code
calc_raw_het Man page Source code
calc_raw_maf Man page 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
cbind.calc_genoprob Man page Source code
cbind.scan1 Man page Source code
cbind.scan1perm Man page Source code
cbind.sim_geno Man page Source code
cbind.viterbi Man page Source code
cbind_expand Man page Source code
cbind_expand_noalign Source code
check4duplicates Source code
check4names Source code
check_binary_pheno Source code
check_cross2 Man page Source code
check_crossinfo Source code
check_crosstype Source code
check_extra_dots Source code
check_founder_geno_size Source code
check_handle_x_chr Source code
check_is_female_vector Source code
check_kinship Source code
check_kinship_onechr Source code
check_new_ids Source code
chisq_colpairs Man page Source code
chr_lengths Man page Source code
chr_names Man page Source code
clean Man page Source code
clean.calc_genoprob Man page
clean.scan1 Man page
clean_genoprob Man page Source code
clean_scan1 Man page Source code
cluster_lapply Source code
collapse_chr_lengths_to_AX Source code
colnames4attr Source code
combine_markers_with_pseudomarkers Source code
compare_geno Man page Source code
compare_genoprob Man page Source code
compare_genoprob_add_annotation Source code
compare_maps Man page Source code
convert2cross2 Man page Source code
convert_cross_info Source code
convert_sex Source code
convert_sexcodes Source code
count_invalid_genotypes Source code
count_xo Man page Source code
covar_names Man page Source code
create_empty_founder_geno Source code
create_gene_query_func Man page Source code
create_marker_index Source code
create_pseudomarker_names Source code
create_snpinfo Man page Source code
create_variant_query_func Man page 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_incomplete_markers Source code
drop_markers Man page Source code
drop_nullmarkers Man page Source code
drop_xcovar Source code
est_herit Man page Source code
est_map Man page Source code
expand_genoprobs_intcovar Source code
expand_interval_to_markers Source code
expand_snp_results Source code
extract_dim_from_header Source code
find_common_ids Source code
find_ibd_segments Man page Source code
find_index_snp Man page Source code
find_intervals Source code
find_lin_indep_cols Source code
find_map_gaps Man page Source code
find_marker Man page Source code
find_markerpos Man page Source code
find_matching_cols Source code
find_peaks Man page Source code
find_peaks_and_bayesint Source code
find_peaks_and_lodint Source code
firstcol2rownames 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
founders Man page Source code
gen_strat_perm Source code
geno2intervals Source code
geno_names Source code
genocol_to_snpcol Source code
genoprob_to_alleleprob Man page Source code
genoprob_to_snpprob Man page Source code
genoprobs_by_contrasts Source code
genoprobs_col2drop Source code
get_common_ids Man page Source code
get_permutation Source code
get_x_covar Man page Source code
grab_dots Source code
guess_phase Man page Source code
handle_null_crossinfo Source code
handle_null_isfemale Source code
handle_null_isxchr Source code
hsq_dimnames Source code
imf Source code
imf.cf Source code
imf.h Source code
imf.k Source code
imf.m Source code
ind_ids Man page Source code
ind_ids_covar Man page Source code
ind_ids_geno Man page Source code
ind_ids_gnp Man page Source code
ind_ids_pheno Man page Source code
index_batches_by_omits Source code
index_snps Man page Source code
infer_f1_geno Source code
insert_pseudomarkers Man page Source code
insert_pseudomarkers_grid Source code
insert_pseudomarkers_minimal Source code
insert_pseudomarkers_onechr Source code
interp_genoprob Man page Source code
interp_genoprob_onechr Source code
interp_map Man page Source code
interpolate_map Source code
invert_founder_index Source code
invert_sdp Man page Source code
is.cross2 Source code
is_cluster Source code
is_kinship_decomposed Source code
is_kinship_list Source code
is_nonneg_number Source code
is_null_weights Source code
is_number Source code
is_phase_known Source code
is_pos_number Source code
is_same Source code
is_web_file Source code
isnt_karl Source code
kinship_bychr2loco Source code
locate_xo Man page Source code
lod_int Man page Source code
map2chr Source code
map2markernames Source code
map2pos Source code
map2rf Source code
map_to_boundaries Source code
map_to_grid Man page Source code
map_to_index Source code
map_to_xpos Source code
marker_names Man page Source code
mat2strata Man page Source code
match_ids Source code
matrix_x_3darray Source code
matrix_x_matrix Source code
matrix_x_vector Source code
max.compare_geno Man page
max.scan1 Man page Source code
max_compare_geno Man page Source code
max_scan1 Man page Source code
maxall_scan1 Source code
maxlod Man page Source code
maxmarg Man page Source code
mf Source code
mf.cf Source code
mf.h Source code
mf.k Source code
mf.m Source code
mpp_decode_geno Source code
mpp_encode_alleles Source code
mpp_geno_names Source code
mpp_is_het Source code
myround Source code
n_chr Man page Source code
n_cores Source code
n_covar Man page Source code
n_founders Man page Source code
n_ind Man page Source code
n_ind_covar Man page Source code
n_ind_geno Man page Source code
n_ind_gnp Man page Source code
n_ind_pheno Man page Source code
n_mar Man page Source code
n_missing Man page Source code
n_pheno Man page Source code
n_phenocovar Man page Source code
n_typed Man page Source code
nalleles Source code
need_founder_geno Source code
normalize_kinship Source code
null_binary_clean Source code
nullrss_clean Source code
permute_ivector Source code
permute_ivector_stratified Source code
permute_nvector Source code
permute_nvector_stratified Source code
pheno2matrix Source code
pheno_names Man page Source code
phenocovar_names Man page Source code
plot.calc_genoprob Man page Source code
plot.compare_geno Man page
plot.scan1 Man page Source code
plot.scan1coef Man page Source code
plot_coef Man page Source code
plot_coefCC Man page Source code
plot_coef_and_lod Source code
plot_compare_geno Man page Source code
plot_genes Man page Source code
plot_genoprob Man page Source code
plot_genoprob_internal Source code
plot_genoprobcomp Man page Source code
plot_lodpeaks Man page Source code
plot_onegeno Man page Source code
plot_peaks Man page Source code
plot_pxg Man page Source code
plot_scan1 Man page Source code
plot_sdp Man page Source code
plot_snpasso Man page Source code
plot_snpasso_and_genes Source code
plot_snpasso_and_sdp Source code
plot_snpasso_sdp_genes Source code
predict_snpgeno Man page Source code
print.cross2 Man page Source code
print.summary.compare_geno Man page Source code
print.summary.cross2 Source code
print.summary.scan1perm Man page Source code
print_aligned Source code
probs_to_grid Man page Source code
pull_genoprobint Man page Source code
pull_genoprobpos Man page Source code
pull_markers Man page Source code
qtl2 Man page
qtl2-internal Man page
qtl2-package Man page
qtl2_temp_dir Source code
qtl2version Man page Source code
random_int Source code
rbind.calc_genoprob Man page Source code
rbind.scan1 Man page Source code
rbind.scan1perm Man page Source code
rbind.sim_geno Man page Source code
rbind.viterbi Man page Source code
read_control_file Source code
read_cross2 Man page Source code
read_csv Man page Source code
read_csv_numer Man page Source code
read_header Source code
read_mult_csv Source code
read_pheno Man page Source code
read_phenocovar Source code
recode_geno Source code
recode_snps Man page Source code
reduce_map_gaps Man page Source code
reduce_markers Man page Source code
reduce_markers_onechr Source code
reduce_to_index_snps Source code
reorder_map_table Source code
replace_ids Man page Source code
replace_ids.calc_genoprob Man page Source code
replace_ids.cross2 Man page Source code
replace_ids.data.frame Man page
replace_ids.matrix Man page Source code
replace_ids.sim_geno Man page Source code
replace_ids.viterbi Man page Source code
rev_snp_index Source code
rqtl1_chrtype Source code
rqtl1_crosstype Source code
rqtl_getgenonames Source code
rqtl_getid Source code
rqtl_getsex Source code
rqtl_nind Source code
rqtl_pull_map Source code
rqtl_reviseXdata Source code
scale_kinship Man page 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
scan1max Man page Source code
scan1max_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
sdp2char Man page Source code
setup_cluster Source code
sim_geno Man page Source code
sim_geno2 Source code
snpinfo_to_map Source code
snpprob_from_cross Source code
split_geno Source code
split_map Source code
sqrt_weights Source code
stop_if_no_file Source code
subset.calc_genoprob Man page Source code
subset.cross2 Man page Source code
subset.scan1 Man page
subset.sim_geno Man page Source code
subset.viterbi Man page Source code
subset_chr Source code
subset_ind Source code
subset_kinship Source code
subset_scan1 Man page Source code
subtractlog Source code
summary.compare_geno Man page
summary.cross2 Man page Source code
summary.scan1perm Man page Source code
summary_compare_geno Man page Source code
summary_scan1perm Man page Source code
test_check_geno Source code
test_emit Source code
test_emitmatrix Source code
test_founder_geno_values Source code
test_init Source code
test_initvector Source code
test_ngen Source code
test_nrec Source code
test_possible_gen Source code
test_step Source code
test_stepmatrix Source code
top_snps Man page Source code
tot_mar Man page Source code
viridis_qtl2 Source code
viterbi Man page Source code
viterbi2 Source code
weight_array Source code
weight_kinship Source code
weight_matrix Source code
weight_vector Source code
weighted_3darray Source code
weighted_matrix Source code
write_control_file Man page Source code
xpos_scan1 Man page Source code
zip_datafiles Man page Source code
rqtl/qtl2 documentation built on Sept. 15, 2021, 12:40 a.m.