keyProfiler-class: Class '"keyProfiler"'

In wokai/spliceSites: A bioconductor package for exploration of alignment gap positions from RNA-seq data

Description

Internal class that counts occurrence of profile factors (e.g. gender male and female) successively for added key-tables. The columns of the key-tables define the groups (e.g. genomic positions: seqid, start, end) for each all profile factors are counted.

Objects from the Class

Objects can be created by calls of the form new("annAligns", ...).

Slots

ev:

Environment: contains the main data of each object. The environment contains the data.frames 'dtb' (key-tabled profiles) and 'prof' (profiles: a table that contains the profile definition for each added key-table) as well as 'groupExpr', an unevaluated Expression which does the data.frame-grouping after addition of a new key-table.

unique:

Logical: When true, there can be maximal one table added for each indexed profile

counted:

Logical: Stores the information which profile already has been counted. Is only used when 'unique' is 'TRUE'.

useValues:

Logical: When TRUE, the object tables the values given together with each key-table, otherwise the profiles are simply counted.

Methods

addKeyTable

signature(x = "keyProfiler",keyTable="data.frame",index="numeric",values="numeric"): Adds keyed data to key-table and counts values according to profile (which is defined by index via profile table).

getKeyTable

signature(x = "keyProfiler"): Returns key-table.

appendKeyTable

signature(x = "keyProfiler",keytable="data.frame",prefix="character",valFactor="numeric",rateFactor="numeric",digits="numeric"): cbinds internal key-table to keytable-argument. A prefix can be added to column-names. A given valFactor is multiplied with the counted values. A given rateFactor causes counted values to be converted into rates (i.e. divided by column-sums and multiplied with rateFactor value. Values are rounded when a digits argument is provided.)

Author(s)

Wolfgang Kaisers

Examples

# Loads profile, position data (key) and aggregated values (ku) data.frames
load(system.file("extdata", "key.RData", package="spliceSites"))
# Group positions
kpc<-new("keyProfiler",keyTable=key1[,c("seqid","lend","rstart")],prof=prof)
addKeyTable(kpc,keyTable=key2[,c("seqid","lend","rstart")],
                index=2,values=key2$nAligns)
addKeyTable(kpc,keyTable=key3[,c("seqid","lend","rstart")],
                index=4,values=key3$nAligns)
cp<-appendKeyTable(kpc,ku,prefix="c.")

wokai/spliceSites documentation built on May 4, 2019, 9:46 a.m.