Description Usage Arguments Value
This function summarizes for each simulation the consistency of the fold changes comparing copy numbers to TPMs, and then the consistency comparing the ALR transformation of the copy numbers versus that of the TPMs.
1 | summarize_abs_sim_runs(abs_sim_runs_list, num_runs, de_probs, dir_probs)
|
abs_sim_runs_list, |
the output from |
num_runs, |
the number of simulations |
de_probs, |
vector of probabilities of differential expression |
dir_probs, |
vector of probabilities of differential expression being increased, given a transcript that is changing |
a data frame with the following columns:
run_num: which simulation?
de_prob: probability of differential expression
dir_prob: probability of DE being up
rel*: the number of transcripts with each category of consistency between copy numbers and relative TPMs
rel_apparent_fc: the apparent fold change of relative TPMs of transcripts that are not changing
adj*: the number of transcripts with each category of consistency between copy numbers and DESeq-normalized counts
adj_apparent_fc: the apparent fold change of DESeq-normalized counts for transcripts that are not changing
alr: the number of transcripts that have consistent changes after ALR transformation of copy numbers vs relative TPMs
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