ssvMakeMembTable-methods: generic for methods to convert various objects to a logical...

In jrboyd/seqsetvis: Set Based Visualizations for Next-Gen Sequencing Data

generic for methods to convert various objects to a logical matrix indicating membership of items (rows) in sets (columns)

Description

generic for methods to convert various objects to a logical matrix indicating membership of items (rows) in sets (columns)

list of character vectors input

GRangesList input

GRanges with mcols input

DataFrame input

matrix of logicals, membership table

data.frame input, final output The final method for all inputs, checks column names and returns logical matrix

Usage

ssvMakeMembTable(object)

## S4 method for signature 'list'
ssvMakeMembTable(object)

## S4 method for signature 'GRangesList'
ssvMakeMembTable(object)

## S4 method for signature 'GRanges'
ssvMakeMembTable(object)

## S4 method for signature 'DataFrame'
ssvMakeMembTable(object)

## S4 method for signature 'matrix'
ssvMakeMembTable(object)

## S4 method for signature 'data.frame'
ssvMakeMembTable(object)

Arguments

object

the object to convert. Supported types: list (of character or GRanges), GRanges with membership table metadata, GRangesList, data.frame/matrix/DataFrame of membership table

Value

a logical matrix indicating membership of items (rows) in sets (columns)

Examples

char_list = list(letters[1:3], letters[2:4])
ssvMakeMembTable(char_list)
library(GenomicRanges)
gr_list = list(GRanges("chr1", IRanges(1:3*2, 1:3*2)),
    GRanges("chr1", IRanges(2:4*2, 2:4*2)))
ssvMakeMembTable(gr_list)
library(GenomicRanges)
gr_list = list(GRanges("chr1", IRanges(1:3*2, 1:3*2)),
    GRanges("chr1", IRanges(2:4*2, 2:4*2)))
ssvMakeMembTable(GRangesList(gr_list))
gr = GRanges("chr1", IRanges(1:3*2, 1:3*2))
gr$set_a = c(TRUE, TRUE, FALSE)
gr$set_b = c(FALSE, TRUE, TRUE)
ssvMakeMembTable(gr)
gr = GRanges("chr1", IRanges(1:3*2, 1:3*2))
gr$set_a = c(TRUE, TRUE, FALSE)
gr$set_b = c(FALSE, TRUE, TRUE)
ssvMakeMembTable(mcols(gr))
memb_mat =  matrix(c(TRUE, TRUE, FALSE, FALSE, TRUE, FALSE, TRUE, FALSE),
    ncol = 2, byrow = FALSE)
ssvMakeMembTable(memb_mat)
memb_df = data.frame(a = c(TRUE, TRUE, FALSE, FALSE),
    b = c(TRUE, FALSE, TRUE, FALSE))
ssvMakeMembTable(memb_df)

jrboyd/seqsetvis documentation built on Dec. 10, 2024, 11:23 a.m.