Deprecated: Deprecated functionality

In ensembldb: Utilities to create and use Ensembl-based annotation databases

Description

All functions, methods and classes listed on this page are deprecated and might be removed in future releases.

GeneidFilter creates a GeneIdFilter. Use GeneIdFilter from the AnnotationFilter package instead.

GenebiotypeFilter creates a GeneBiotypeFilter. Use GeneBiotypeFilter from the AnnotationFilter package instead.

EntrezidFilter creates a EntrezFilter. Use EntrezFilter from the AnnotationFilter package instead.

TxidFilter creates a TxIdFilter. Use TxIdFilter from the AnnotationFilter package instead.

TxbiotypeFilter creates a TxBiotypeFilter. Use TxBiotypeFilter from the AnnotationFilter package instead.

ExonidFilter creates a ExonIdFilter. Use ExonIdFilter from the AnnotationFilter package instead.

ExonrankFilter creates a ExonRankFilter. Use ExonRankFilter from the AnnotationFilter package instead.

SeqNameFilter creates a SeqNameFilter. Use SeqNameFilter from the AnnotationFilter package instead.

SeqstrandFilter creates a SeqStrandFilter. Use SeqStrandFilter from the AnnotationFilter instead.

SeqstartFilter creates a GeneStartFilter, TxStartFilter or ExonStartFilter depending on the value of the parameter feature. Use GeneStartFilter, TxStartFilter and ExonStartFilter instead.

SeqendFilter creates a GeneEndFilter, TxEndFilter or ExonEndFilter depending on the value of the parameter feature. Use GeneEndFilter, TxEndFilter and ExonEndFilter instead.

Usage

GeneidFilter(value, condition = "==")

GenebiotypeFilter(value, condition = "==")

EntrezidFilter(value, condition = "==")

TxidFilter(value, condition = "==")

TxbiotypeFilter(value, condition = "==")

ExonidFilter(value, condition = "==")

ExonrankFilter(value, condition = "==")

SeqnameFilter(value, condition = "==")

SeqstrandFilter(value, condition = "==")

SeqstartFilter(value, condition = ">", feature = "gene")

SeqendFilter(value, condition = "<", feature = "gene")

Arguments

value	The value for the filter.
condition	The condition for the filter.
feature	For SeqstartFilter and SeqendFilter: on what type of feature should the filter be applied? Supported are "gene", "tx" and "exon".

ensembldb documentation built on Nov. 8, 2020, 4:57 p.m.