qtl2-package	qtl2-package
add_threshold	add_threshold
align_scan1_map	qtl2-internal
basic_summaries	basic_summaries
batch_cols	batch_cols
batch_vec	batch_vec
bayes_int	bayes_int
c.scan1perm	rbind.scan1perm
calc_entropy	calc_entropy
calc_errorlod	calc_errorlod
calc_genoprob	calc_genoprob
calc_geno_freq	calc_geno_freq
calc_grid	calc_grid
calc_het	calc_het
calc_hotspots	calc_hotspots
calc_kinship	calc_kinship
calc_raw_founder_maf	calc_raw_founder_maf
calc_raw_geno_freq	calc_raw_geno_freq
calc_raw_het	calc_raw_het
calc_raw_maf	calc_raw_maf
calc_sdp	calc_sdp
cbind.calc_genoprob	cbind.calc_genoprob
cbind.phasedgeno	cbind.phasedgeno
cbind.scan1	cbind.scan1
cbind.scan1perm	cbind.scan1perm
cbind.sim_geno	cbind.sim_geno
cbind.viterbi	cbind.viterbi
cbind_expand	cbind_expand
CCaltcolors	CCcolors
CCcolors	CCcolors
CCorigcolors	CCcolors
check_cross2	check_cross2
chisq_colpairs	chisq_colpairs
chr_lengths	chr_lengths
chr_names	basic_summaries
clean	clean
clean.calc_genoprob	clean_genoprob
clean.scan1	clean_scan1
clean_genoprob	clean_genoprob
clean_scan1	clean_scan1
compare_founder_geno	compare_founder_geno
compare_geno	compare_geno
compare_genoprob	compare_genoprob
compare_maps	compare_maps
convert2cross2	convert2cross2
count_xo	count_xo
covar_names	basic_summaries
create_gene_query_func	create_gene_query_func
create_snpinfo	create_snpinfo
create_variant_query_func	create_variant_query_func
decomp_kinship	decomp_kinship
drop_markers	drop_markers
drop_nullmarkers	drop_nullmarkers
est_herit	est_herit
est_map	est_map
find_dup_markers	find_dup_markers
find_ibd_segments	find_ibd_segments
find_index_snp	find_index_snp
find_map_gaps	find_map_gaps
find_marker	find_marker
find_markerpos	find_markerpos
find_peaks	find_peaks
fit1	fit1
founders	basic_summaries
fread_csv	fread_csv
fread_csv_numer	fread_csv_numer
genoprob_to_alleleprob	genoprob_to_alleleprob
genoprob_to_snpprob	genoprob_to_snpprob
get_common_ids	get_common_ids
get_x_covar	get_x_covar
guess_phase	guess_phase
index_snps	index_snps
ind_ids	basic_summaries
ind_ids_covar	basic_summaries
ind_ids_geno	basic_summaries
ind_ids_gnp	basic_summaries
ind_ids_pheno	basic_summaries
insert_pseudomarkers	insert_pseudomarkers
interp_genoprob	interp_genoprob
interp_map	interp_map
invert_sdp	invert_sdp
locate_xo	locate_xo
lod_int	lod_int
map_to_grid	map_to_grid
marker_names	basic_summaries
mat2strata	mat2strata
max.compare_geno	max_compare_geno
max.scan1	max_scan1
maxlod	maxlod
maxmarg	maxmarg
max_compare_geno	max_compare_geno
max_scan1	max_scan1
n_chr	basic_summaries
n_covar	basic_summaries
n_founders	basic_summaries
n_ind	basic_summaries
n_ind_covar	basic_summaries
n_ind_geno	basic_summaries
n_ind_gnp	basic_summaries
n_ind_pheno	basic_summaries
n_mar	basic_summaries
n_missing	n_missing
n_pheno	basic_summaries
n_phenocovar	basic_summaries
n_typed	n_missing
phenocovar_names	basic_summaries
pheno_names	basic_summaries
plot.calc_genoprob	plot_genoprob
plot.compare_geno	plot_compare_geno
plot.scan1	plot_scan1
plot.scan1coef	plot_coef
plot_ci	plot_ci
plot_cistrans	plot_cistrans
plot_coef	plot_coef
plot_coefCC	plot_coef
plot_colorscale	plot_colorscale
plot_compare_geno	plot_compare_geno
plot_genes	plot_genes
plot_geno	plot_geno
plot_genoprob	plot_genoprob
plot_genoprobcomp	plot_genoprobcomp
plot_lodpeaks	plot_lodpeaks
plot_onegeno	plot_onegeno
plot_peaks	plot_peaks
plot_pxg	plot_pxg
plot_scan1	plot_scan1
plot_scan1_heatmap	plot_scan1_heatmap
plot_sdp	plot_sdp
plot_snpasso	plot_snpasso
predict_snpgeno	predict_snpgeno
print.cross2	print.cross2
print.summary.compare_geno	summary_compare_geno
print.summary.scan1perm	print.summary.scan1perm
probs_to_grid	probs_to_grid
pull_genoprobint	pull_genoprobint
pull_genoprobpos	pull_genoprobpos
pull_markers	pull_markers
qtl2	qtl2-package
qtl2-internal	qtl2-internal
qtl2version	qtl2version
rbind.calc_genoprob	rbind.calc_genoprob
rbind.phasedgeno	rbind.phasedgeno
rbind.scan1	rbind.scan1
rbind.scan1perm	rbind.scan1perm
rbind.sim_geno	rbind.sim_geno
rbind.viterbi	rbind.viterbi
read_cross2	read_cross2
read_pheno	read_pheno
recode_snps	recode_snps
reduce_map_gaps	reduce_map_gaps
reduce_markers	reduce_markers
replace_ids	replace_ids
replace_ids.calc_genoprob	replace_ids
replace_ids.cross2	replace_ids
replace_ids.data.frame	replace_ids
replace_ids.matrix	replace_ids
replace_ids.sim_geno	replace_ids
replace_ids.viterbi	replace_ids
scale_kinship	scale_kinship
scan1	scan1
scan1blup	scan1blup
scan1coef	scan1coef
scan1gen	scan1gen
scan1max	scan1max
scan1perm	scan1perm
scan1snps	scan1snps
sdp2char	sdp2char
sim_geno	sim_geno
smooth_gmap	smooth_gmap
subset.calc_genoprob	subset.calc_genoprob
subset.cross2	subset.cross2
subset.phasedgeno	subset.phasedgeno
subset.scan1	subset_scan1
subset.sim_geno	subset.sim_geno
subset.viterbi	subset.viterbi
subset_scan1	subset_scan1
summary.compare_geno	summary_compare_geno
summary.cross2	summary.cross2
summary.scan1perm	summary_scan1perm
summary_compare_geno	summary_compare_geno
summary_scan1perm	summary_scan1perm
top_snps	top_snps
tot_mar	basic_summaries
unsmooth_gmap	unsmooth_gmap
viterbi	viterbi
write_control_file	write_control_file
xpos_scan1	xpos_scan1
zip_datafiles	zip_datafiles
[.calc_genoprob	subset.calc_genoprob
[.cross2	subset.cross2
[.phasedgeno	subset.phasedgeno
[.sim_geno	subset.sim_geno
[.viterbi	subset.viterbi
