View source: R/centromere_telomere.R
centromere.telomere.analysis | R Documentation |
Calculate a scaled matrix of the interchromosomal interactions aligned from centromere to telomere
centromere.telomere.analysis(
exp,
chrom.vec,
nrow = 100,
leave.out = NULL,
q.top = 1e-05,
verbose = F
)
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. |
40kb
Elzo de Wit, e.d.wit@nki.nl
## 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)
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