read_eager_stats_table: Extract poseidon information from the general stats table of...
In sidora-tools/eager2poseidon: Automatically fill in Missing Metadata in a Janno File
View source: R/read_eager_results.R
read_eager_stats_table R Documentation
Extract poseidon information from the general stats table of a run
Description
Extract poseidon information from the general stats table of a run
Usage
read_eager_stats_table(general_stats_fn, tsv_data, snp_cutoff = 50)
Arguments
general_stats_fn
character. Path to the MultiQC general stats table.
Can be found in multiqc/multiqc_data/multiqc_general_stats.txt within the specified eager output directory (--outdir).
tsv_data
A tibble containing information from the eager TSV. Created with read_eager_tsv
snp_cutoff
integer. The minimum number of SNPs used for nuclear contamination results, for the results to be
considered trustworthy. Any values from libraries with fewer than this number of SNPs are ignored.
Value
A tibble containing the poseidon janno fields of Damage, Nr_SNPs, Endogenous, Contamination,
Contamination_Err, Contamination_Meas, and Contamination_Note
sidora-tools/eager2poseidon documentation built on May 12, 2023, 11:58 p.m.
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View source: R/read_eager_results.R
| read_eager_stats_table | R Documentation |
Extract poseidon information from the general stats table of a run
Description
Extract poseidon information from the general stats table of a run
Usage
read_eager_stats_table(general_stats_fn, tsv_data, snp_cutoff = 50)
Arguments
general_stats_fn |
character. Path to the MultiQC general stats table.
Can be found in multiqc/multiqc_data/multiqc_general_stats.txt within the specified eager output directory ( |
tsv_data |
A tibble containing information from the eager TSV. Created with read_eager_tsv |
snp_cutoff |
integer. The minimum number of SNPs used for nuclear contamination results, for the results to be considered trustworthy. Any values from libraries with fewer than this number of SNPs are ignored. |
Value
A tibble containing the poseidon janno fields of Damage, Nr_SNPs, Endogenous, Contamination, Contamination_Err, Contamination_Meas, and Contamination_Note
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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