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

Global functions
CCcolors Man page
CCorigcolors Man page
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
[.calc_genoprob Man page
[.cross2 Man page
[.sim_geno Man page
[.viterbi Man page
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
alleleprob_to_snpprob 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
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_entropy Man page Source code
calc_errorlod Man page Source code 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 Source code
calc_genoprob2 Source code Source code
calc_grid Man page Source code
calc_grid_onechr Source code
calc_hsq_clean Source code
calc_kinship Man page Source code 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_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.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 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 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 Source code
check_kinship Source code
check_kinship_onechr Source code
check_new_ids Source code
chisq_colpairs Man page Source code 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 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 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 Source code
count_xo Man page Source code Source code
count_xo_3d 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_variant_query_func Man page Source code
crosstype_supported 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 Source code
est_map2 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 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 Source code
find_peaks_and_bayesint Source code Source code
find_peaks_and_lodint Source code 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
gen_strat_perm Source code
geno2intervals Source code
geno_names Source code
genocol_to_snpcol Source code
genoprob_to_alleleprob Man page Source code 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
get_x_covar Man page Source code Source code
grab_dots Source code
guess_phase Man page Source code
guess_phase_A Source code
guess_phase_X Source code
guess_phase_f2A Source code
guess_phase_f2X 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 Source code
lod_int Man page Source code
lod_int_plain 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 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
n_chr Man page Source code
n_cores Source code
n_covar 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
nterp_genoprob_onechr 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
pheno2matrix Source code
pheno_names Man page Source code
phenocovar_names Man page Source code
plot.calc_genoprob Man page Source code
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_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_snpasso Man page Source code
plot_snpasso_and_genes Source code
predict_snpgeno Man page Source code 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
reduce_map_gaps Man page Source code
reduce_markers Man page Source code 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.sim_geno Man page Source code
replace_ids.viterbi Man page Source code
rev_snp_index 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
s_phase_known 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
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
sim_geno Man page Source code Source code
sim_geno2 Source code 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 Source code
viterbi2 Source code 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 Nov. 6, 2018, 7:01 a.m.