Main class containing file paths, scores and values for spike normalization. It inherits from ChIPSeqSpikeCore.
experimentList: A list of Experiment objects
ChIPSeqSpikeDataset(endogenousBam_vec, exogenousBam_vec, bigWigFile_endogenous_vec, inputBigWigFile, inputBamFile, expnames, inputSF = 0, inputNb = 0, SetArrayList = list(), matBindingList = list())
Character vector of file paths to the BAM files aligned to the reference genome.
Character vector of file paths to the BAM files aligned to the exogenous genome.
Character vector of file paths to the bigWig files aligned to the reference genome.
String representing the file path to the input control bigWig file. (see details)
String representing the file path to the input control BAM file.
Character vector of experiment names. (see details)
Numeric scaling factor. Default is 0. (see details)
Numeric read counts. Default is 0. (see details)
List of PlotSetArray objects. Default is an empty list. (see details)
List of binding value matrices. Default is an empty list. (see details)
Returns the input BAM path
Returns the input bigWig path
Returns a character vector of paths to the experiment bigWig files
Returns a character vector of experiment names
Returns the input scaling factor
Returns the number of reads contained in the input BAM file
Returns a list of PlotSetArray objects. (see details)
Returns a list of matrices containing binding values. (see details)
Get the Experiment object at index i
Modifies the input scaling factor value
Modifies the input count value
Modifies the input bigWig file path
Modifies the PlotSetArray list. (see details)
Modifies the list of binding value matrices. (see details)
x[[i]] <- value
value to ChIPSeqSpikeDataset i
'expnames' character vector is used to define the names of the experiment list and are used as labels in plotting, summary and getRatio functions.
'inputSF' is the scaling factor that will be applied to the input bigWigFile before input subtraction of the different experiments. 'inputNb' which holds the number of aligned reads is used to calculate the aforementioned factor. Only the endogenous count and factor are needed for the input conversely to the experiments for which both the endogenous/exogenous scaling factors and counts are needed to perform spike-in normalization.
'SetArrayList' contains PlotSetArray objects. The PlotSetArray class is defined in the Bioconductor package 'seqplots' and holds the values that are necessary to plot profiles and heatmaps. These values can be retrieved with the 'getAverageBindingValues' function.
'matBindingList' contains matrices of binding values for each experiment. These values are used to generate boxplots and correlations plots. They are retrieved by calling the function 'BWGFile_summary' of the bioconductor package 'rtracklayer'.
If the dataset contains more than one input, one would want to use the ChIPSeqSpikeDatasetList class. Boost mode classes (ChIPSeqSpikeDatasetBoost and ChIPSeqSpikeDatasetListBoost) can also be considered to speed up the analysis.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
file_vec <- system.file("extdata", c("bam_files/H3K79me2_0_dm3-filtered.bam", "bam_files/H3K79me2_0_hg19-filtered.bam", "bigwig_files/H3K79me2_0-filtered.bw", "bigwig_files/input_0-filtered.bw", "bam_files/input_0_hg19-filtered.bam"), package="ChIPSeqSpike") csds <- ChIPSeqSpikeDataset(endogenousBam_vec = file_vec, exogenousBam_vec = file_vec, bigWigFile_endogenous_vec = file_vec, inputBigWigFile = file_vec, inputBamFile = file_vec, expnames = "H3K79me2_0") csds
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.