API for IoannisVardaxis/MACPET
Model based analysis for paired-end data

Global functions
AnalysisStatistics Man page Source code
Assess_Interaction_fun_Rcpp Source code
BigMat_SP_fun Source code
BlackListCorrection_fun Source code
Break_output_fun Source code
BuildBowtieIndex_fun Source code
Check_BAM_Header_fun Source code
Check_BiProd_fun_Rcpp Source code
Check_If_sorted_fun Source code
ConvertToPE_BAM Man page Source code
ConvertToPSelf Man page Source code
ConvertToPSelf.GInteractions Man page Source code
ConvertToPSelf.default Man page Source code
Convert_Filter_CreateFastq_main_fun Source code
Convert_Filter_CreateFastq_sub_fun Source code
Create_ConnectionPETsData_fun Source code
Create_GenomeMapObject Source code
Create_InteractionStructures_fun Source code
Create_Networks_fun Source code
Create_fastq_list_fun Source code
Dijkstra_GSP_fun_Rcpp Source code
FilterFastqYield_fun_Rcpp Source code
FindInter_fun Source code
FindIntra_fun Source code
FindRegions_fun Source code
FindSelf_fun Source code
FitCallGlobal_fun Source code
FitCallLocal_fun_Rcpp Source code
FixMatesFlags_fun Source code
FixMates_main_fun Source code
GInteractionsCovnert_fun Source code
GenomeMap Man page
GenomeMap-class Man page
GetSAMFiles_fun Source code
GetShortestPath Man page Source code
GetShortestPath.GenomeMap Man page Source code
GetShortestPath.default Man page Source code
GetSignInteractions Man page Source code
GetSignInteractions.GenomeMap Man page Source code
GetSignInteractions.default Man page Source code
Get_ChromCombData_fun Source code
Get_ExpectedPETs_fun Source code
Get_InteractionInfo_fun_Rcpp Source code
Get_LatestInteraction_fun Source code
Get_NewPeakSummit_fun_Rcpp Source code
Get_PETsInfoMat_fun_Rcpp Source code
Get_PETsSplit_fun Source code
Get_PETsStats_fun Source code
Get_Paired_Yields_fun Source code
Get_Paired_names_fun Source code
Get_PeaksSplit_fun Source code
Get_QCellCombCounts_fun Source code
Get_QCellCombCounts_fun_Rcpp Source code
Get_QCellPETCounts_fun_Rcpp Source code
Get_QuantileChunks_fun Source code
Get_SignificanceCall_Data_fun Source code
Get_VectPosIndex_Vectorized_fun_Rcpp Source code
Get_VectPosIndex_fun_Rcpp Source code
Get_Vij_Data_fun Source code
Get_image_S0_fun Source code
Get_image_S1_P1_fun Source code
Get_image_S1_P2_fun Source code
Get_image_S2_P1_fun Source code
Get_image_S2_P2_fun Source code
Get_image_S2_P3_fun Source code
Get_image_S3_P1_fun Source code
Get_image_S3_P2_fun Source code
Get_image_S3_P3_fun Source code
Get_image_S3_P4_fun Source code
Get_image_S4_P1_fun Source code
Initiate_GenomeMap_fun_Rcpp Source code
Initiate_InteractionInfMat_fun_Rcpp Source code
InputCheckMACPETUlt Source code
Input_check_S0_fun Source code
Input_check_S1_fun Source code
Input_check_S2_fun Source code
Input_check_S3_fun Source code
Input_check_S4_fun Source code
Input_check_SA_fun Source code
LoadBAM_FromInputChecks_fun Source code
LoadBAM_FromMACPETUlt_fun Source code
MACPET Man page
MACPET-package Man page
MACPETUlt Man page Source code
MACPET_GenomeMapData.rda Man page
MACPET_pinterData.rda Man page
MACPET_pintraData.rda Man page
MACPET_pselfData.rda Man page
MACPET_psfitData.rda Man page
Map_fastq_V0_main_fun Source code
Map_fastq_V0_sub_fun Source code
Map_fastq_V1_main_fun Source code
Map_fastq_V1_sub_fun Source code
MergeBAMfiles_fun Source code
PInter Man page
PInter-class Man page
PIntra Man page
PIntra-class Man page
PSFit Man page
PSFit-class Man page
PSelf Man page
PSelf-class Man page
Parse_fastqfiles_main_fun Source code
PeaksToGRanges Man page Source code
PeaksToGRanges.PSFit Man page Source code
PeaksToGRanges.default Man page Source code
PeaksToNarrowPeak Man page Source code
PeaksToNarrowPeak.PSFit Man page Source code
PeaksToNarrowPeak.default Man page Source code
Poiss_fun Source code
PoissonLocalInference_fun Source code
Prepare_InteractionsData_fun Source code
RegionIds_fun Source code
Run_InteractionAnalysis_fun Source code
SAMtoBAM_convert_fun Source code
SampleChIAPETData.bam Man page
SampleChIAPETDataRead_1.bam Man page
SampleChIAPETDataRead_2.bam Man page
Save_BigMat_fun_Rcpp Source code
SepSelfIntra_fun Source code
SignificanceCall_fun Source code
SmoothSplines_fun Source code
SortBAMQname_fun Source code
Stage_0_Main_fun Source code
Stage_1_Main_fun Source code
Stage_2_Main_fun Source code
Stage_3_Main_fun Source code
Stage_4_Main_fun Source code
SubsetSignificantInteractions_fun_Rcpp Source code
TagsToGInteractions Man page Source code
TagsToGInteractions.PSFit Man page Source code
TagsToGInteractions.default Man page Source code
TakeFitAnalysisData_fun Source code
Update_Network_fun Source code
Update_Network_kh_fun Source code
Update_ToBeAddedInter_fun_Rcpp Source code
exportPeaks Man page Source code
exportPeaks.PSFit Man page Source code
exportPeaks.default Man page Source code
plot Man page
plot.GenomeMap Man page Source code
plot.PInter Man page Source code
plot.PIntra Man page Source code
plot.PSFit Man page Source code
plot.PSelf Man page Source code
summary Man page
summary.GenomeMap Man page Source code
summary.PInter Man page Source code
summary.PIntra Man page Source code
summary.PSFit Man page Source code
summary.PSelf Man page Source code
IoannisVardaxis/MACPET documentation built on Aug. 11, 2018, 11 a.m.