Filter-class: Filter results fetched from the miRNA host genes database

In jotsetung/mirhostgenes: mirhostgenes: putting miRNAs into genomic context

Description

These classes allow to specify which entries (i.e. mature miRNAs, pre-miRNAs etc. should be retrieved from the database).

Details

Description of filters (in alphabetical order).

AlignmentIdFilter

Allows to filter results based on the (internal) alignment ID for a pre-miRNA. The same pre-miRNA sequence might have multiple genomic alignments, thus, the alignment ID was introduced ensure an unique identifier in the database. Both, the mature miRNAs and the host transcripts are linked via this ID to the pre-miRNA alignment.

ArrayFilter

Allows to filter results based on provided microarray names (e.g. "HG-U133_Plus_2"). Use the method listArrays to get a list of available microarray names.

DatabaseFilter

Allows to restrict results to genes/transcripts defined in the speciefied databases. Since the database contains gene/transcripts defined in various databases (e.g. Ensembl, Vega, NCBI RefSeq) restricting the results to one database helps avoiding redundant gene/transcript definitions. Use the method listDatabases to get a list of supported values.

MarmirnaConfidence

Allows to filter on the confidence information for mature and pre-miRNAs stored in the miRBase. Requires that the corresponding information have been extracted from the miRBase and inserted into the MirhostDb database. Note that miRBase prior version 21 did not provide mature miRNA confidence information. Also, at present, the filter allows only to filter the query to fetch only high confidence (by specifying value="high") miRNAs.

MatMirnaFilter

Filter on the mature miRNA names (e.g. "hsa-miR-15b-5p")

MatMirnaIdFilter

Filter on the mature miRNA identifiers (i.e. mirbase accession numbers, e.g. "MIMAT0000062").

PositionFilter

Allows to filter results based on whether the (mature) miRNA is exonic or intronic, i.e. is encoded in an exon of the transcript, or in an intron.

PreMirnaConfidence

See MatMirnaConfidence above for a description. In contrast to mature miRNAs, also miRBase versions prior to version 21 did provide high confidence information.

PreMirnaFilter

Allows to filter on pre-miRNA names (e.g. "hsa-mir-15b").

PreMirnaIdFilter

Allows to filter on pre-miRNA identifiers (mirbase accession numbers, e.g. "MI0000060").

ProbesetIdFilter

Allows to filter on microarray probe set IDs.

ReadCountFilter

Allows to filter the results by the number of reads from various high throughput sequencing experiments mapping to the mature or pre-miRNAs.

In addition to the above classes all Filter classes defined in the ensembldb package. See the vignette for a more detailed description.

Value

See method descriptions above for the return values.

Objects from the Class

While objects can be created by calls e.g. of the form new("PositionFilter", ...) users are strongly encouraged to use the specific functions: AlignmentIdFilter, ArrayFilter, DatabaseFilter, MatMirnaConfidence, MatMirnaFilter, MatMirnaIdFilter, MirfamFilter and MirfamIdFilter, PositionFilter, PreMirnaConfidence PreMirnaFilter, PreMirnaIdFilter, ProbesetIdFilter and ReadCountFilter. See examples below for usage.

Slots

condition

Object of class "character": can be either "=", "in" or "like" to filter on character values (e.g. gene id, gene biotype, seqname etc), or "=", ">" or "<" for numerical values (chromosome/seq coordinates). Note that for "like" value should be a SQL pattern (e.g. "ENS%" that matches all values starting with "ENS").

match.case

Object of class "logical": for PreMirnaFilter and MatMirnaFilter specifying whether case sensitive or in-sensitive queries should be performed for the pre-miRNA or mature miRNA names.

of

For ReadCountFilter: spefifying the database table in which the read counts are stored (i.e. either "pre_mirna" or "mat_mirna").

value

Object of class "character": the value to be used for filtering.

Extends

Class "AnnotationFilter" defined in the AnnotationFilter package.

Methods

(in alphabetic order)

column

signature(object = "PositionFilter", db = "MirhostDb", with.tables="character"): returns the column (table column name in the miRNA host genes database) to be used for the filtering. The method can be applied to any filter class defined in the mirhostgenes or ensembldb packages. Argument with.tables allows to restrict the filter to be applied to certain database tables. By default the filter is applied to all database tables.

The method returns a character string with the name of the column.

condition

Get the condition of the filter (i.e. how values should be compared).

The condition method returns a character string representing the condition.

value

Get the value of the filter.

The value method returns a character vector of the value(s).

where

signature(object = "PositionFilter", db = "MirhostDb", with.tables="character"): returns the where clause for the SQL call to the miRNA host genes database. The method can be applied to any filter class defined in the mirhostgenes or ensembldb packages. Argument with.tables allows to restrict the filter to be applied to certain database tables. By default the filter is applied to all database tables.

The method returns the SQL where clause that will be used to restrict the results returned by the database. This string is dependent on the type of database.

Note

All methods for filter classes (also those defined in the AnnotationFilter package, i.e. GeneIdFilter, GenenameFilter, GeneBiotypeFilter, TxIdFilter, TxBiotypeFilter, SeqNameFilter, SeqStrandFilter, should include the MirhostDb class instance as this will cause the methods (column and where) to return values specific for the layout of the miRNA host genes database. See examples below for more details.

Author(s)

Johannes Rainer

See Also

GeneIdFilter, SeqNameFilter, GeneIdFilter (in the mirhostgenes package).

Examples

library(MirhostDb.Hsapiens.v75.v20)
mhdb <- MirhostDb.Hsapiens.v75.v20

## Create a filter that could be used to retrieve all informations for
## the respective gene.
Gif <- GeneIdFilter("ENSG00000012817")
Gif
## Returns the where clause of the SQL querys specific for the
## mirhostgenes database
where(Gif, mhdb)

## Create a filter for a chromosomal end position of a gene
Sef <- SeqEndFilter(10000, condition=">", "gene")
Sef

## Get and set the value of a filter.
value(Sef)

## In the miRNA host genes database we are rather interested to get
## pre-miRNAs from certain genomic positions, thus we define "pre_mirna"
## as the feature and call where by supplying also the MirhostDb
## object
Sef <- SeqEndFilter(1000, condition=">", "pre_mirna")
where(Sef, mhdb)

## Get all high confidence pre-miRNAs.
premirnas(mhdb, filter=PreMirnaConfidence("high"))

## Get all mature miRNAs with more than 1000 reads across all experiments
matmirnas(mhdb, filter=ReadCountFilter(1000, of="mat_mirna"))

jotsetung/mirhostgenes documentation built on May 19, 2019, 9:42 p.m.