GPSEA cohort analysis

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 #} {% for count in hpo_counts %} {% endfor %}

Top {{top_hpo_count}} HPO terms

A total of {{ cohort.count_distinct_hpo_terms() }} HPO terms were used to annotated the cohort. {% if n_has_onset_info %} {# Optional onset info #} {{ n_has_onset_info }} had onset information for at least 20% of individuals. {% endif %}
HPO Term ID Seen in n individuals
{{ count['label'] }} {{ count['term_id'] }} {{ count['count'] }}
{# The table is inconsistent. Skip it for now! {% if n_has_onset_info > 0 %}

Top {{top_var_count}} HPO Terms

A total of {{ cohort.count_distinct_hpo_terms() }} HPO terms were used to annotated the cohort.

{% for onset_info in has_onset_information %} {% endfor %}
HPO Count
{{ onset_info.display_label }} {{ onset_info.count }}
{% endif %} #} {# The most common variants #} {% for count in var_counts %} {% endfor %}

Top {{top_var_count}} variants

Variants are shown according to {{ transcript_id }}. A total of {{ cohort.all_variant_infos() | count | pluralize('unique variant') }} were identified in the cohort.
Seen in n individuals Variant key Variant Name Protein Effect Variant Class
{{ count['count'] }} {{ count['key'] }} {{ count['hgvsc'] }} {{ count['hgvsp'] }} {{ count['effects'] }}
{# The most common diseases #} {% for disease_count in disease_counts %} {% endfor %}

Diseases

Name ID N diagnosed individuals
{{ disease_count['label'] }} {{ disease_count['disease_id'] }} {{ disease_count['count'] }}
{# The most common variant effects #} {% if has_transcript %} {% for effect in variant_effects %} {% endfor %}

Variant categories for {{ transcript_id }}

Variant effect Annotation count Percent
{{ effect['effect'] }} {{ effect['count'] }} {{ effect['percent'] }}%
{% else %}

Call this function with transcript to see table with variant effect counts.

{% endif %}