See_GEM_formatter: GEMINI data formatter

In davemcg/see_gem: Integrate 'GEMINI' (and 'peddy') Output into Interactive Html Document

Description

Formats data for reactive knit document made with knit_see_gem

Usage

See_GEM_formatter(GEMINI_data, core_fields = c("test", "pos_id",
  "impact_so", "gene", "hgvsc", "hgvsp", "aaf", "gno_af_all",
  "exac_num_hom_alt", "clinvar_id", "rs_ids", "GoogleScholar"),
  in_silico = c("test", "pos_id", "gene", "impact_so", "cadd_phred",
  "ccr_pct_v1", "revel", "polyphen_score", "sift_score",
  "metalr_rankscore", "genesplicer", "spliceregion", "linsight"),
  genotypes = c("test", "pos_id", "gene", "impact_so", "family_members",
  "family_genotypes"),
  extra_columns_to_retain = "^gno|rankscore$|*num*|^clin|*domain*|*codon*",
  linkify = "yes", underscore_to_space = "yes")

Arguments

GEMINI_data	The data frame / tibble of your GEMINI data. All tests (e.g. autosomal_recessive, compound_het) collapsed into a single data frame with the GEMINI sub command test given in a 'test' column.
core_fields	These are the columns that will be shown by default
in_silico	These are in silico consequence columns (e.g CADD, SIFT)
genotypes	These columns show the full genotype information for each person in the family.
extra_columns_to_retain	These are columns not selected above that will be retained. This is a regular expression, so you can give this something like '^gno|rankscore$|*num*' and all columns starting with 'gno' or ending with 'rankscore' or containing 'num' will be selected.
linkify	Do you want to turn format fields as hyperlinks? Hard-coded to position id (gnomAD), gene (OMIM), ClinVar ID (ClinVar), rs_id (dbSNP).
underscore_to_space	Do you want to replace underscores with spaces?

Value

None

Examples

## Not run: 
GEMINI_data <- data.table::rbindlist(gemini_test_wrapper('/path/to/gemini.db', 
'autosomal_recessive', families = 'the_fam'),
gemini_test_wrapper('/path/to/gemini.db', 'autosomal_dominant', filter = 
"aaf < 0.05 AND aaf_esp_all < 0.001 AND aaf_1kg_all < 0.001 AND 
af_exac_all < 0.001 AND 
(is_coding=1 OR is_splicing=1 OR impact_severity='HIGH') AND 
filter is NULL" , families = 'the_fam'))
See_GEM_formatter(GEMINI_data)

## End(Not run)

davemcg/see_gem documentation built on May 15, 2019, 2:50 a.m.