bigWigFile: Set the path to the bigwig file

Description Usage Arguments Details Value Author(s) Examples

Description

Set the path to the input or experiment bigwig file.

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
bigWigFile(theObject) <- value
            
            
## S4 replacement method for signature 'ChIPSeqSpikeDataset'
bigWigFile(theObject) <- value

## S4 replacement method for signature 'ChIPSeqSpikeDatasetBoost'
bigWigFile(theObject) <- value

## S4 replacement method for signature 'Experiment'
bigWigFile(theObject) <- value

## S4 replacement method for signature 'ExperimentLoaded'
bigWigFile(theObject) <- value

## S4 replacement method for signature 'ChIPSeqSpikeCore'
bigWigFile(theObject) <- value

Arguments

theObject

A ChIPSeqSpikeCore, ChIPSeqSpikeDataset, ChIPSeqSpikeDatasetBoost, Experiment or ExperimentLoaded object

value

A string representing a path to a bigwig file

Details

If the object is ChIPSeqSpikeCore, ChIPSeqSpikeDataset or ChIPSeqSpikeDatasetBoost, bigWigFile will set the path to the input DNA experiment bigwig file corresponding to all experiments defined by the object.

If the object is Experiment or ExperimentLoaded, bigWigFile will set the path to the experiment bigwig file.

Value

The modified object is returned

Author(s)

Nicolas Descostes

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
info_file_csv <- system.file("extdata/info.csv", package="ChIPSeqSpike")
bam_path <- system.file("extdata/bam_files", package="ChIPSeqSpike")
bigwig_path <- system.file("extdata/bigwig_files", package="ChIPSeqSpike")
gff_vec <- system.file("extdata/test_coord.gff", package="ChIPSeqSpike")
genome_name <- "hg19"
output_folder <- "test_chipseqspike"
bigwig_files <- system.file("extdata/bigwig_files", 
                            c("H3K79me2_0-filtered.bw",
                              "H3K79me2_100-filtered.bw",
                              "H3K79me2_50-filtered.bw",
                              "input_0-filtered.bw",
                              "input_100-filtered.bw",
                              "input_50-filtered.bw"), package="ChIPSeqSpike")

## Copying example files
dir.create("./test_chipseqspike")
result <- file.copy(bigwig_files, "test_chipseqspike")

if(.Platform$OS.type != 'windows') {
    csds <- spikePipe(info_file_csv, bam_path, bigwig_path, gff_vec, 
                      genome_name, verbose = TRUE, 
                      outputFolder = output_folder)
    write("toto", file="./test_chipseqspike/toto.bw")
    getBigWigFile(csds[[1]][[1]])
    bigWigFile(csds[[1]][[1]]) <- "test_chipseqspike/toto.bw"
    getBigWigFile(csds[[1]][[1]])
}

unlink("test_chipseqspike/", recursive = TRUE)

ChIPSeqSpike documentation built on Nov. 8, 2020, 5:29 p.m.