Successfully loaded {{ cohort | count | pluralize('individual') }}. {# Sex #} {{ cohort.count_males() | was_were }} recorded as male, {{ cohort.count_females() }} as female, and {{ cohort.count_unknown_sex() }} as unknown sex. {# Vital status #} {% if cohort | count == cohort.count_unknown_vital_status() %} No information about individuals' vital status was reported. {% else %} {{ cohort.count_alive() | was_were }} reported to be alive at the time of last encounter, {{ cohort.count_deceased() | was_were }} deceased, and vital status was unreported for {{ cohort.count_unknown_vital_status() | pluralize('individual')}}. {% endif %} {# HPO terms #} The cohort included {{ cohort.count_distinct_hpo_terms() | pluralize('HPO term') }}. {# Disease and age at last encounter #} {{ cohort.count_with_disease_onset() | pluralize('individual')}} had disease onset information and {{ cohort.count_with_age_of_last_encounter() }} had information about the age of last encounter. {# Measurements #} {% if cohort.all_measurement | count > 0 %} Information was provided for {{ cohort.all_measurement | count | pluralize('measurement assay') }}. {% endif %}
{% if cohort.get_excluded_count() > 0 %}Not able to load {{ cohort.get_excluded_count() }} individuals.
{% else %}No errors encountered.
{% endif %} {# The most common HPO terms #}HPO Term | ID | Seen in n individuals |
---|---|---|
{{ count['label'] }} | {{ count['term_id'] }} | {{ count['count'] }} |
A total of {{ cohort.count_distinct_hpo_terms() }} HPO terms were used to annotated the cohort.
HPO | Count |
---|---|
{{ onset_info.display_label }} | {{ onset_info.count }} |
Seen in n individuals | Variant key | Variant Name | Protein Effect | Variant Class |
---|---|---|---|---|
{{ count['count'] }} | {{ count['key'] }} | {{ count['hgvsc'] }} | {{ count['hgvsp'] }} | {{ count['effects'] }} |
Name | ID | N diagnosed individuals |
---|---|---|
{{ disease_count['label'] }} | {{ disease_count['disease_id'] }} | {{ disease_count['count'] }} |
Variant effect | Annotation count | Percent |
---|---|---|
{{ effect['effect'] }} | {{ effect['count'] }} | {{ effect['percent'] }}% |
Call this function with transcript to see table with variant effect counts.
{% endif %}