Possibility - class which represents the abundance of the isoform (or isoform sub-element, such as a junction or exon) in human tissues, cell lines, or disease-relevant samples.
Original code (now deleted) input the GTEx data and had transcript abundances across ~30 human tissues (see below).
This class may be helpful for comparing abundances of events (e.g., exon skipping) versus whole-isoforms. It may be helpful in comparing short-read-based versus long-read-based expression values.
It could also be used to plot expression visualizations in the isoform imager module. For example - Farilie's Swan program has an example.
def __init__(self, expr_dict):
self.expr_dict = expr_dict # tissue -> rpkm
self.avg_expr = self.compute_avg_expr()
def __getitem__(self, tiss):
# when expr_obj fetch by key (tissue), return value
return self.expr_dict[tiss]
def compute_avg_expr(self):
tot = 0
for k, v in self.expr_dict.items():
v = float(v)
tot += v
avg_expr = tot/len(self.expr_dict)
return avg_expr```
Possibility - class which represents the abundance of the isoform (or isoform sub-element, such as a junction or exon) in human tissues, cell lines, or disease-relevant samples.
Original code (now deleted) input the GTEx data and had transcript abundances across ~30 human tissues (see below).
This class may be helpful for comparing abundances of events (e.g., exon skipping) versus whole-isoforms. It may be helpful in comparing short-read-based versus long-read-based expression values.
It could also be used to plot expression visualizations in the isoform imager module. For example - Farilie's Swan program has an example.