centromere.telomere.analysis: centromere.telomere.analysis

In robinweide/GENOVA: GENOVA: expore the Hi-C

centromere.telomere.analysis

Description

Calculate a scaled matrix of the interchromosomal interactions aligned from centromere to telomere

Usage

centromere.telomere.analysis(
  exp,
  chrom.vec,
  nrow = 100,
  leave.out = NULL,
  q.top = 1e-05,
  verbose = F
)

Arguments

exp	GENOVA data structure for your experiment of interest
chrom.vec	a vector containing the chromosomes that should be considered in the pair-wise interchromosomal interactions
nrow	dimensions of the matrix (number of columns will be the same)
leave.out	two-column matrix or data.frame containing the specific chromosome combinations that need to left out
q.top	top quantile of scores that should be left out of the analysis (because they are outliers)
verbose	Produces a progress-indication.

Resolution recommendation

40kb

Author(s)

Elzo de Wit, [e-mail]

Examples

## Not run: 
# Get a scaled matric of the interchomosomal interactions between 15 and 19
out1519 <- centromere.telomere.analysis(WT_40kb,
  chrom.vec = c("chr15", "chr19")
)

# Plot the results
draw.centromere.telomere(out1519)

## End(Not run)

robinweide/GENOVA documentation built on March 14, 2024, 11:16 p.m.