compute.oncoscore.from.region {OncoScore} | R Documentation |
Perform OncoScore analysis on a given chromosomic region
compute.oncoscore.from.region(chromosome, start = NA, end = NA, gene.num.limit = 100, filter.threshold = NA, analysis.mode = "Log2", cutoff.threshold = 21.09, file = NULL)
chromosome |
chromosome to be retireved |
start |
initial position to be used |
end |
final position to be used |
gene.num.limit |
A limit to the genes to be considered in the analysis; this is done to limit the number of queries to PubMed |
filter.threshold |
threshold to filter for a minimum number of citations for the genes |
analysis.mode |
logaritmic scores to be computed, i.e., log10, log2, natural log or log5 |
cutoff.threshold |
threshold to be used to asses the oncogenes |
file |
should I save the results to text files? |
the computed scores
chromosome = 15 start = 200000 end = 300000 compute.oncoscore.from.region(chromosome, start, end)