R wrapper for Progenetix


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Documentation for package ‘pgxRpi’ version 1.0.0

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hg19_bins A dataframe containing location information for 1MB-size bins within the hg19 genome. This dataset is generated based on the accessed cytoband data and used for CNV frequency calculation from local pgxseg files.
hg19_cytoband A dataframe containing cytoband annotation details extracted from the hg19 gennome. It is used for CNV frequency visualization.
hg38_bins A dataframe containing location information for 1MB-size bins within the hg38 genome. This dataset is generated based on the accessed cytoband data and used for CNV frequency calculation from local pgxseg files.
hg38_cytoband A dataframe containing cytoband annotation details extracted from the hg38 gennome. It is used for CNV frequency visualization.
pgxCount Count samples in one collation of a given filter
pgxFilter Query available filters
pgxFreqplot Plot CNV frequency data
pgxLoader Load data from Progenetix database
pgxSegprocess Extract, analyse and visualize "pgxseg" files