BlastReport-class: Class '"BlastReport"'

In gschofl/blastr: A wrapper for NCBI Blast

Description

An S4 class that that serves as the top-level container for data parsed from NCBI BLAST XML output. It contains the following top-level components:

• BlastHeader

• BlastParameters

• QueryList

Usage

## S4 method for signature 'BlastReport'
getHeader(x, ...)

## S4 method for signature 'BlastReport'
getParams(x)

## S4 method for signature 'BlastReport'
getQuery(x, i, drop = TRUE)

## S4 method for signature 'BlastReport'
getHit(x, i, drop = TRUE)

## S4 method for signature 'BlastReport'
nhits(x)

## S4 method for signature 'BlastReport'
getQueryNum(x)

## S4 method for signature 'BlastReport'
getQueryID(x)

## S4 method for signature 'BlastReport'
getQueryDef(x)

## S4 method for signature 'BlastReport'
getQueryLen(x)

## S4 method for signature 'BlastReport'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'BlastReport'
x[[i, j, ...]]

## S4 method for signature 'BlastReport'
is.na(x)

## S4 method for signature 'BlastReport'
show(object)

Details

The Query elements store results from individual BLAST queries. Each Query holds a HitList with possibly multiple Hits, which, in turn, can contain multiple high-scoring pairs (Hsps).

Queries, Hits, and Hsps can be extracted using the accessors getQuery, getHit, and getHsp, or by directly subsetting a BlastReport object.

E.g. report[[1]][[1]] will return the first hit in the first query.

The show methods for various blast objects can be modified by a number of global options. Specifically, the number of Hits shown when displaying Querys or HitLists are set by showHits. Whether alignments are displayed or not is controlled by showAlignment. Setting these options to NULL, restores the defaults.

See the general documentation of show method for the expected behavior.

Methods (by generic)

• getHeader: Return BlastHeader.

• getParams: Return BlastParameters.

• getQuery: Return Query or QueryList.

• getHit: Return a list of HitLists.

• nhits: Returns the numbers of hits; <numeric>.

• getQueryNum: Return query numbers; <integer>.

• getQueryID: Return query IDs; <character>.

• getQueryDef: Return query definitions; <character>.

• getQueryLen: Return query lengths; <integer>.

• [: Subset to return an QueryList.

• [[: Subset to return an Query.

• is.na: Indicate missing Querys.

• show:

Slots

header

Header information; BlastHeader.

params

Blast parameters and statistics BlastParameters.

queries

Queries; QueryList.

See Also

The constructor blastReport; the BLAST classes BlastReportDB and BlastTable

show

Examples

# options("showHits" = 20)
# show(hitlist)
# options("showHits" = NULL)
# show(hitlist)

gschofl/blastr documentation built on May 17, 2019, 8:52 a.m.