The Spearman method is based on rankings. More precisely, it is defined as the covariance of two variables divided by the product of their standard deviation. The Pearson method measures the metric differences between samples and is therefore influenced by outliers. We offer two different functions for the correlation computation: Pearson or Spearman. (-1 indicates perfect anti-correlation, 1 perfect correlation.) The result of the correlation computation is a table of correlation coefficients that indicates how “strong” the relationship between two samples is and it will consist of numbers between -1 and 1. The ENCODE blacklist page ( ) contains useful information about regions with unusually high countsthat may be worth removing. Bins with abnormally high reads counts artificially increase pearson correlation that’s why, multiBamSummary tries to remove outliers using the median absolute deviation (MAD) method applying a threshold of 200 to only consider extremely large deviations from the median. If set, bins with very large counts are removed. The available options are: png, eps, pdf and svg. If given, this option overrides the image format based on the plotFile ending. Possible choices: png, pdf, svg, eps, plotly Title of the plot, to be printed on top of the generated image. Multiple labels have to be separated by spaces, e.g. User defined labels instead of default labels from file names. svg.īy setting this option, genomic regions that have zero or missing (nan) values in all samples are excluded. The file extension determines the format, so heatmap.pdf will save the heatmap in PDF format.
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