Description Usage Arguments Value Examples
Extract results tables from multiple hap.py result objects and combine
into a single data.frame
. Source information from each
result is added as an additional column (happy_prefix
).
1 2 3 | extract_results(happy_result_list, table = c("summary", "extended",
"pr.all", "pr.indel.pass", "pr.indel.sel", "pr.indel.all", "pr.snp.pass",
"pr.snp.sel", "pr.snp.all"))
|
happy_result_list |
A |
table |
Table of data to extract from each result.
|
a data.frame
of combined tables from list
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | ## Not run:
samplesheet <- readr::read_csv("group_id,replicate_id,happy_prefix
PCR-Free,NA12878-I30,NA12878-I30_S1
PCR-Free,NA12878-I33,NA12878-I33_S1
Nano,NA12878-R1,NA12878-R1_S1
Nano,NA12878-R2,NA12878-R2_S1
")
hap_samplesheet <- read_samplesheet_(samplesheet = samplesheet_df)
# get collapsed summary table of high-level metrics
summary_df <- extract_results(hap_samplesheet$results, table = "summary")
unique(summary_df$happy_prefix)
# [1] "/output/path/prefix" "/different/path/prefix"
## End(Not run)
|
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