S4 classes for QTL summary statistics and metadata

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Documentation for package ‘QTLExperiment’ version 1.0.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

.mashData_2_qtle	Coercing mash data objects into QTLe objects
.mashFit_2_qtle	Coercing mash data objects into QTLe objects
betas	Named assay getters and setters
betas-method	Named assay getters and setters
betas<-	Named assay getters and setters
betas<--method	Named assay getters and setters
cbind-method	Combining QTLExperiment objects
coerce-method	An S4 class to represent QTL summary statistics.
colData-method	Internal QTLExperiment functions
errors	Named assay getters and setters
errors-method	Named assay getters and setters
errors<-	Named assay getters and setters
errors<--method	Named assay getters and setters
feature_id	Named rowData getters and setters
feature_id-method	Named rowData getters and setters
feature_id<-	Named rowData getters and setters
feature_id<--method	Named rowData getters and setters
int_colData	Internal QTLExperiment functions
int_colData-method	Internal QTLExperiment functions
int_colData<-	Internal QTLExperiment functions
int_colData<--method	Internal QTLExperiment functions
int_metadata	Internal QTLExperiment functions
int_metadata-method	Internal QTLExperiment functions
int_metadata<-	Internal QTLExperiment functions
int_metadata<--method	Internal QTLExperiment functions
int_rowData	Internal QTLExperiment functions
int_rowData-method	Internal QTLExperiment functions
int_rowData<-	Internal QTLExperiment functions
int_rowData<--method	Internal QTLExperiment functions
lfsrs	Named assay getters and setters
lfsrs-method	Named assay getters and setters
lfsrs<-	Named assay getters and setters
lfsrs<--method	Named assay getters and setters
mainExpName	Return the name of a QTLExperiment object.
mainExpName-method	Return the name of a QTLExperiment object.
mainExpName<-	Return the name of a QTLExperiment object.
mainExpName<--method	Return the name of a QTLExperiment object.
mash2qtle	Coercing mash data objects into QTLe objects
mockMASHR	Mock data for the QTLExperiment object
mockMASHR_FIT	Mock data for the QTLExperiment object
mockQTLE	Mock data for the QTLExperiment object
mockSummaryStats	Mock data for the QTLExperiment object
objectVersion	Return the version of a QTLExperiment object
objectVersion-method	Return the version of a QTLExperiment object
parallel_slot_names-method	Internal QTLExperiment functions
pvalues	Named assay getters and setters
pvalues-method	Named assay getters and setters
pvalues<-	Named assay getters and setters
pvalues<--method	Named assay getters and setters
qtle-assays	Named assay getters and setters
QTLe-coerce	Coercing mash data objects into QTLe objects
qtle-col_ids	Named colData getters and setters
QTLe-combine	Combining QTLExperiment objects
QTLe-internals	Internal QTLExperiment functions
QTLe-name	Return the name of a QTLExperiment object.
QTLe-recover	Recover QTLExperiment IDs
qtle-row_ids	Named rowData getters and setters
QTLe-subset	Subsetting and replacing data in QTLExperiment objects
QTLe-version	Return the version of a QTLExperiment object
QTLExperiment	An S4 class to represent QTL summary statistics.
QTLExperiment-class	An S4 class to represent QTL summary statistics.
rbind-method	Combining QTLExperiment objects
recover_qtle_ids	Recover QTLExperiment IDs
rowData-method	Internal QTLExperiment functions
state_id	Named colData getters and setters
state_id-method	Named colData getters and setters
state_id<-	Named colData getters and setters
state_id<--method	Named colData getters and setters
sumstats2qtle	Coerce QTL summary statistics into a QTLExperiment object
updateObject	Update a QTLExperiment object
updateObject-method	Update a QTLExperiment object
variant_id	Named rowData getters and setters
variant_id-method	Named rowData getters and setters
variant_id<-	Named rowData getters and setters
variant_id<--method	Named rowData getters and setters
[-method	Subsetting and replacing data in QTLExperiment objects
[<--method	Subsetting and replacing data in QTLExperiment objects