View source: R/facets-wrapper.R
procSample | R Documentation |
Processes the output from preProcSample for given cval and min.nhet
procSample(x, cval = 150, min.nhet = 15, dipLogR = NULL)
x |
the output from preProcSample; should contain seg.tree and jointseg |
cval |
critical value for segmentation |
min.nhet |
minimum number of heterozygote snps in a segment used for bivariate t-statistic during clustering of segments |
dipLogR |
diploid level obtained from a fit, typically using a higher cval, can be used with lower cval to recover focal changes |
The minor copy number lcn may not be estimated with confidence when a segment has fewer than min.nhet heterozygous SNPs and hence will return NA. If there are too few heterozygous SNPs in a segment then mafR and mafR.clust can be NA.
jointseg |
The data that were segmented. Only the loci that were sampled within a snp.nbhd are present |
out |
data frame of segment summaries pre and post clustering of segments. The columns are: chrom the chromosome to which the segment belongs; seg the segment number; num.mark the number of SNPs in the segment; nhet the number of SNPs that are deemed heterozygous; cnlr.median the median log-ratio of the segment; mafR the log-odds-ratio summary for the segment; segclust the segment cluster to which segment belongs; cnlr.median.clust the median log-ratio of the segment cluster; mafR.clust the log-odds-ratio summary for the segment cluster; cf the cellular fraction of the segment; tcn the total copy number of the segment; lcn the minor copy number of the segment. |
dipLogR |
specified or obtained from data |
... |
other output when findDiploidLogR is used |
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