sd.plot: Plotting delta scores

In lgl15/cnmtf: Prioritisation of single nucleotide variants using Corrected non-negative matrix tri-factorisation

Description

Function to plot dispersion plots, manhattan plots and venn diagrams of SNP sds

Usage

sd.plot(R.snps = rownames(R), object.sd = NULL, work.dat = NULL,
  pvals.lrm = NULL, alpha.lrm = NULL, snps.known1 = NULL,
  snps.known2 = NULL, maf.snps = NULL, kd.snps = NULL,
  snps.fp.lrm = NULL, print.file = NULL, tao.sd = NULL,
  clus.a = list(c(1)), clus.b = list(c(2)), trait.project = NULL,
  tmap = NULL, ylim.sd = c(-10, 10))

Arguments

R.snps	List of SNPs in the original seed files
object.sd	Results from function sd.score
work.dat	Working directory
pvals.lrm	P-values obtained in a LRM
alpha.lrm	Significance level
snps.known1	List of known associations
snps.known2	List of known associations 2
maf.snps	Minor allele frequencies of SNPs in the original R matrix without filtering
kd.snps	Node degress of SNPs in the original Wu matrix without filtering
snps.fp.lrm	Potential False Positive association from LRM
print.file	File to print plots
tao.sd	Treshold of SD
clus.a	List of patient clusters to use in the delta scores
trait.project	Trait/outcome
tmap	Mapping of SNPs to genes, chr and genomic position
ylim.sd	Limits for y axis

Value

• Plots printed to print.file

• sig.snp.nmtf, sig.snp.lrm : Significant SNV ids from cNMTF and LRM

Author(s)

Luis G. Leal, [e-mail]

See Also

Other Scoring functions: analyze.cnmtf, custom.venn, delta.score, manhattan.plot, manhattan.table, plot.clusters, rec.list, sd.score

lgl15/cnmtf documentation built on May 28, 2019, 6:33 p.m.