getCorrelations {NADfinder} | R Documentation |
Get correlations and p-values between biological replicates based on coverage signal for peak regions. The signals will be filtered by the background cutoff value before calculated correlations. This function also output a correlation plots using the corrplot.
getCorrelations( se, chr = paste0("chr", seq_len(19)), ratioAssay = "ratio", window = 10000L, cutoff = 1, method = c("spearman", "pearson", "kendall"), file_name = "Correlation plots.pdf", ... )
se |
A RangedSummarizedExperiment object. The output from log2se. |
chr |
A vector of character. Filter for seqnames. It should be the chromosome names to be kept. |
ratioAssay |
character(1). Column name of ratio for correlation calculation. |
window |
numeric(1) or integer(1). The window size for summary of the ratios. |
cutoff |
numeric(1). All the coverage signals lower than cutoff value in a given window will be filtered out. |
method |
character(1) indicating which correlation coefficient is to be computed. See cor. |
file_name |
A file name for output correlation plots |
... |
Parameters not used. |
A list of matrixes of correlation coefficients and p-values.
Jianhong Ou, Haibo Liu
data(triplicate.count) se <- triplicate.count se <- log2se(se, transformation = "log2CPMRatio", nucleolusCols = c("N18.subsampled.srt-2.bam", "N18.subsampled.srt-3.bam", "N18.subsampled.srt.bam"), genomeCols = c("G18.subsampled.srt-2.bam", "G18.subsampled.srt-3.bam", "G18.subsampled.srt.bam")) getCorrelations(se, chr="chr18")