voila tsv output description

[Kerr Welton]

Hi,

I run this command voila tsv $i ../build/splicegraph.sql -f ./${a}.tsv -j 20 and get the tsv output files, there are two columns called "probability_non_changing" and "probability_changing" makes me quite confused, I wonder if there is any description for these columns, and I want to know how to filter the results with p value/q value < 0.05 according to this tsv files？

Looking forward to your reply.

Best wishes,

Kerr

[Paul Jewell]

Hello Kerr,

I think you can find the description in general for these columns in the section here: https://biociphers.bitbucket.io/majiq-docs-academic/gallery/heterogen-vignette.html#Generating-TSV-output

As far as applying additional filters, there are many flags provided by running the command line:

$ voila tsv --help

I will post the relevant ones here:

Thresholds for Deltapsi or Heterogen inputs:
  --changing-between-group-dpsi CHANGING_BETWEEN_GROUP_DPSI
                        For determining changing with HET or dPSI inputs. This is the maximum absolute difference in median values of PSI for HET inputs (or E(dPSI) for dPSI inputs) for which an LSV/junction can be marked changing. The default is "0.2"
  --non-changing-between-group-dpsi NON_CHANGING_BETWEEN_GROUP_DPSI
                        For determining non-changing with HET or dPSI inputs. This is the maximum absolute difference in median values of PSI for HET inputs (or E(dPSI) for dPSI inputs) for which an LSV/junction can be marked non-changing. The default is "0.05"

Thresholds for Deltapsi inputs:
  --threshold THRESHOLD
                        Filter out LSVs with no junctions predicted to change over a certain value. Even when show-all is used this value is still used to calculate the probability in the TSV. The default is "0.2".
  --probability-threshold PROBABILITY_THRESHOLD
                        This is off by default. If set, confidence must be above this probability threshold in addition to the psi threshold.

Thresholds for Heterogen inputs:
  --non-changing-pvalue-threshold NON_CHANGING_PVALUE_THRESHOLD
                        For determining non-changing with HET inputs. Minimum p-value for which an LSV/junction can return true. Uses minimum p-value from all tests provided. The default is "0.05".
  --non-changing-within-group-IQR NON_CHANGING_WITHIN_GROUP_IQR
                        For determining non-changing with HET inputs. Maximum IQR within a group for which an LSV/junction can return true. The default is "0.1".
  --changing-pvalue-threshold CHANGING_PVALUE_THRESHOLD
                        For determining changing with HET inputs. Maximum p-value for which an LSV/junction can return true. Uses maximum p-value from all tests provided. The default is "0.05".

I'm surmising you may want to adjust "changing-pvalue-threshold" or "non-changing-pvalue-threshold"

Let me know if it helps.

Thanks!