Function reference • Longcell

All functions

GLRT(): Generalized likelihood ratio test.

GLRT_sig_plot(): plot for GLRT significant results

HighExprsGene(<Splice>,<numeric>): generic HighExprsGene function for Splice object

HighExprsGene(): generic HighExprsGene function definition

Splice-class: The Splice Class

bbmoment(): bbmoment

beta_dis(): distance between two psi distribution modeled by beta.

beta_mean(): calculate mean value for a beta distribution

beta_var(): calculate variance for a beta distribution

cellGeneSiteCount(): cellGeneSiteCount

creatSplice_from_df(): creatSplice_from_df

createSplice(): createSplice

exon_search(): Search if an exon is within an exon group.

extractExonTable(): build an exon count table for a gene

geneSiteTable(<Splice>,<list>,<character>): generic gene_exons_table function for Splice object

geneSiteTable(): generic geneSiteTable function definition

geneSiteTable.base(): geneSiteTable.base

geneSiteTable_df(): geneSiteTable_df

geneSitesPhi_from_beta(): geneSitesPhi_from_beta

geneSitesPhi_from_psi(): geneSitesPhi_from_psi

geneSitesPsi(<Splice>,<character>): generic geneSitesPsi function for Splice object

geneSitesPsi(): generic genes_exons_psi function definition

geneSitesPsi.base(): geneSitesPsi.base

gene_GLRT(<Splice>,<character>,<vector>,<vector>): generic gene_GLRT function for Splice object

gene_GLRT(): generic gene_GLRT function definition

gene_GLRT.base(): Generalized likelihood ratio test for a gene.

genesSitesPhi(<Splice>,<character>): generic genesSitesPhi function for Splice object

genesSitesPhi(): generic genesSitesPhi function definition

genesSitesPhi.base(): compute phi for exons in multi-genes

genes_groups_GLRT(<Splice>,<character>,<list>,<list>): generic genes_groups_GLRT function for Splice object

genes_groups_GLRT(): generic genes_groups_GLRT function definition

genes_groups_GLRT.base(): Generalized likelihood ratio test for multiples gene.

genes_multigroups_GLRT(): genes_multigroups_GLRT

getIsoform(<Splice>,<character>): generic getIsoform function for Splice object

getIsoform(): generic getIsoform function definition

getIsoform.base(): extract isoforms

getMetaSites(): getMetaSites

isoform2bases(): isoform2bases

isoform2sites(): isoform2sites

junction_count(): junction_count

ll(): ll

metaSite-class: The metaSite Class

metaSpliceSite(): metaSpliceSite

metasite_retrieve(): metasite_retrieve

mle_bb(): mle_bb

mle_module(): mle_module

moduleExtract(): moduleExtract

phiNabla(): phiNabla

phiPlot(): phiPlot

phi_conf_bootstrap(): phi_conf_bootstrap

phi_conf_delta(): phi_conf_delta

phi_from_beta(): phi_from_beta

phi_from_psi(): phi_from_psi

psiCellPlot(): psiCellPlot

psiCellPlotData(): psiCellPlotData

psiHist(<Splice>,<character>,<character>): generic psiHist function for Splice object

psiHist(): generic psiHist function definition

psiHist.base(): plot psi distribution

range_scale(): range_scale

sashimi(): sashimi

sashimi_plot(): sashimi_plot

sashimi_plot_data(): sashimi_plot_data

siteMerge(): siteMerge

sites2matrix(): sites2matrix

sites2vec(): sites2vec

sites_coef(): sites_coef

sites_coef_matrix(): sites_coef_matrix

spliceTable(): spliceTable