score.filter | R Documentation |
Filtering the scores output from iso.switch
.
score.filter(scores, prob.cutoff = 0.5, diff.cutoff = 1,
t.points.cutoff = 2, pval.cutoff = 0.01, cor.cutoff = 0.5,
data.exp = NULL, mapping = NULL, sub.isoform.list = NULL,
sub.isoform = F, max.ratio = F, x.value.limit = c(9, 17))
scores |
the scores object output from |
prob.cutoff, diff.cutoff, t.points.cutoff, pval.cutoff, cor.cutoff |
the cut-offs corresponding to switch frequencies/probablities, sum of average sample differences, p-value and time points cut-offs for both intervals before and after switch and Pearson correlation. |
data.exp, mapping |
the expression and gene-isoform mapping data. |
sub.isoform.list |
a vector of isoforms to output the corresponding results (see |
sub.isoform |
logical, to output subset of the results(TRUE) or not (FALSE). If TRUE, |
max.ratio |
logical, to show maximum abundant isoform results(TRUE) or not (FALSE). If TRUE, data.exp and mapping data must be
provided to calculate the isoform ratios to the genes using |
x.value.limit |
the region of x axis (time) for investigation. |
Users can set cut-offs, such as for the probability/frequency of switch and sum of average differences, to further refine the switch results.
a table of scores after filtering.
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