Index

A

activateFails() (PascalX.genescorer.chi2sum method)

C

chi2perm (class in PascalX.pathway) chi2rank (class in PascalX.pathway) chi2rank() (PascalX.genexpr.genexpr method)

chi2sum (class in PascalX.genescorer) clean() (PascalX.genescorer.genescorer method) close() (PascalX.snpdb.db method)

D

db (class in PascalX.snpdb)

G

gene_info() (PascalX.genome.genome method) genescorer (class in PascalX.genescorer) genexpr (class in PascalX.genexpr) genome (class in PascalX.genome) get() (PascalX.snpdb.db method) get_ensembl_annotation() (PascalX.genome.genome method) get_geneinfo() (PascalX.genescorer.genescorer method) get_GTEX_expr() (PascalX.genexpr.genexpr method) get_sigpathways() (PascalX.pathway.chi2perm method) (PascalX.pathway.chi2rank method)

get_topscores() (PascalX.genescorer.genescorer method) (PascalX.xscorer.rsum method) (PascalX.xscorer.zsum method) getChrSNPs() (PascalX.refpanel.refpanel method) getKeys() (PascalX.snpdb.db method) getPosatSNPs() (PascalX.snpdb.db method) getSNPatPos() (PascalX.snpdb.db method) getSNPKeys() (PascalX.snpdb.db method) getSNPs() (PascalX.snpdb.db method) getSNPtoChrMap() (PascalX.refpanel.refpanel method) getSortedKeys() (PascalX.snpdb.db method)

I

insert() (PascalX.snpdb.db method)

J

jointlyRank() (PascalX.xscorer.rsum method) (PascalX.xscorer.zsum method)

jointlyRank_mapper() (PascalX.xscorer.rsum method) (PascalX.xscorer.zsum method)

L

load_expr() (PascalX.genexpr.genexpr method) load_genome() (PascalX.genescorer.genescorer method) (PascalX.genexpr.genexpr method) (PascalX.genome.genome method) (PascalX.xscorer.rsum method) (PascalX.xscorer.zsum method) load_GWAS() (PascalX.genescorer.genescorer method) (PascalX.xscorer.rsum method) (PascalX.xscorer.zsum method) load_mapping() (PascalX.genescorer.genescorer method) (PascalX.mapper.mapper method) (PascalX.xscorer.rsum method) (PascalX.xscorer.zsum method)

load_modules() (PascalX.pathway.chi2perm method) (PascalX.pathway.chi2rank method) load_pos_reference() (PascalX.refpanel.refpanel method) load_refpanel() (PascalX.genescorer.genescorer method) (PascalX.xscorer.rsum method) (PascalX.xscorer.zsum method) load_scores() (PascalX.genescorer.genescorer method) (PascalX.xscorer.rsum method) (PascalX.xscorer.zsum method) load_snp_reference() (PascalX.refpanel.refpanel method)

M

mapper (class in PascalX.mapper) matchAlleles() (PascalX.genescorer.genescorer method) (PascalX.xscorer.rsum method) (PascalX.xscorer.zsum method)

matchAlleles_mapper() (PascalX.xscorer.rsum method) (PascalX.xscorer.zsum method)

O

open() (PascalX.snpdb.db method)

P

plot_genesnps() (PascalX.genescorer.chi2sum method) (PascalX.xscorer.rsum method) (PascalX.xscorer.zsum method)

plot_genexpr() (PascalX.genexpr.genexpr method) plot_Manhattan() (PascalX.genescorer.genescorer method)

R

rank() (PascalX.genescorer.genescorer method) rank_mapper() (PascalX.genescorer.genescorer method)

refpanel (class in PascalX.refpanel) rescore() (PascalX.genescorer.chi2sum method) rsum (class in PascalX.xscorer)

S

save_GWAS() (PascalX.genescorer.genescorer method) save_scores() (PascalX.genescorer.genescorer method) (PascalX.xscorer.rsum method) (PascalX.xscorer.zsum method) score() (PascalX.genescorer.chi2sum method) (PascalX.genescorer.wchi2sum method) (PascalX.pathway.chi2perm method) (PascalX.pathway.chi2rank method) (PascalX.xscorer.rsum method) (PascalX.xscorer.zsum method) score_all() (PascalX.genescorer.genescorer method) (PascalX.xscorer.rsum method) (PascalX.xscorer.zsum method)

score_chr() (PascalX.genescorer.genescorer method) (PascalX.xscorer.rsum method) (PascalX.xscorer.zsum method) score_gene_bulk_chr() (PascalX.genescorer.chi2sum method) score_map() (PascalX.xscorer.rsum method) (PascalX.xscorer.zsum method) set_genescorer() (PascalX.pathway.chi2perm method) (PascalX.pathway.chi2rank method) set_refpanel() (PascalX.refpanel.refpanel method)

T

test_gene_assocdir() (PascalX.genescorer.chi2sum method)

W

wchi2sum (class in PascalX.genescorer)

Z

zsum (class in PascalX.xscorer)