summary_sstacks: Summarize STACKS sstacks log file generated by stackr
In thierrygosselin/stackr: Run stacks software pipeline for RADseq analysis inside R
Description
Usage
Arguments
Value
References
See Also
Examples
View source: R/summary_sstacks.R
Description
This function reads the log file of stackr run_sstacks
and summarise the information.
The information shown is particularly helpful when choosing the best thresholds.
This function is run automatically inside run_sstacks, but
it can be run on it's own.
Usage
1
summary_sstacks(sstacks.log, verbose = FALSE)
Arguments
sstacks.log
(path, character).
The cstacks log file generated by run_sstacks.
verbose
(logical, optional) Make the function a little more chatty during
execution.
Default: verbose = FALSE.
Value
When the function is run separately it returns an object in the
global environment and a file in 08_stacks_results folder, if it exists and
if not, the file is written in the working directory.
The summary is a tibble:
INDIVIDUALS: The sample id.
LOCUS_IN_CATALOG: The number of locus in the catalog.
LOCUS_IN_SAMPLES: The number of locus in the sample.
MATCHING_LOCI: The number of matching loci
BLACKLISTED_LOCI_NO_VERIFIED_HAPLOTYPES: The number of loci with no verfied haplotypes.
BLACKLISTED_LOCI_MATCHING_MORE_1_CATALOG_LOCUS: The number of
loci that matched more than one catalog locus and were excluded.
BLACKLISTED_LOCI_UNACCOUNTED_SNP: The number of loci that contained SNPs
unaccounted for in the catalog and were excluded.
HAPLOTYPES_VERIFIED: The number of haplotypes verified by the total
number of haplotypes examined.
GAPPED_ALIGNMENTS_ATTEMPTED: The number of gapped alignments attempted
LOCI_MATCHED_1_CATALOG_LOCUS: The number of loci that matched more than
one catalog locus and were excluded.
HAPLOTYPES_VERIFIED_EXAMINED: The number of haplotypes verified by the total
number of haplotypes examined.
BLACKLISTED_LOCI_MATCHED_NO_CATALOG: The number of loci blacklisted because
of no match with the catalog.
GAPPED_BLACKLISTED_LOCI_MATCHING_MORE_1_CATALOG_LOCUS: The number of
loci that matched more than one catalog locus and were excluded.
GAPPED_BLACKLISTED_LOCI_UNACCOUNTED_SNP: The number of loci that
contained SNPs unaccounted for in the catalog and were excluded.
LOCI_NO_VERIFIED_HAPLOTYPES: The number of loci with no verified haplotypes.
BLACKLISTED_LOCI_INCONSISTENT_ALIGNMENTS: The number of loci blacklisted
because of inconsistent alignments.
TOTAL_SAMPLE_LOCI: This is the number of loci that will be used in
stacks tsv2bam.
References
Catchen JM, Amores A, Hohenlohe PA et al. (2011)
Stacks: Building and Genotyping Loci De Novo From Short-Read Sequences.
G3, 1, 171-182.
Catchen JM, Hohenlohe PA, Bassham S, Amores A, Cresko WA (2013)
Stacks: an analysis tool set for population genomics.
Molecular Ecology, 22, 3124-3140.
See Also
Examples
1
2
3
4
5
6
7
## Not run:
sum <- stackr::summary_sstacks(
sstacks.log = "09_log_files/sstacks_20191101@1108.log",
verbose = TRUE
)
## End(Not run)
thierrygosselin/stackr documentation built on Nov. 11, 2020, 11 a.m.
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Description Usage Arguments Value References See Also Examples
View source: R/summary_sstacks.R
Description
This function reads the log file of stackr run_sstacks
and summarise the information.
The information shown is particularly helpful when choosing the best thresholds.
This function is run automatically inside run_sstacks, but
it can be run on it's own.
Usage
1 | summary_sstacks(sstacks.log, verbose = FALSE)
|
Arguments
sstacks.log |
(path, character).
The cstacks log file generated by |
verbose |
(logical, optional) Make the function a little more chatty during
execution.
Default: |
Value
When the function is run separately it returns an object in the
global environment and a file in 08_stacks_results folder, if it exists and
if not, the file is written in the working directory.
The summary is a tibble:
INDIVIDUALS: The sample id.
LOCUS_IN_CATALOG: The number of locus in the catalog.
LOCUS_IN_SAMPLES: The number of locus in the sample.
MATCHING_LOCI: The number of matching loci
BLACKLISTED_LOCI_NO_VERIFIED_HAPLOTYPES: The number of loci with no verfied haplotypes.
BLACKLISTED_LOCI_MATCHING_MORE_1_CATALOG_LOCUS: The number of loci that matched more than one catalog locus and were excluded.
BLACKLISTED_LOCI_UNACCOUNTED_SNP: The number of loci that contained SNPs unaccounted for in the catalog and were excluded.
HAPLOTYPES_VERIFIED: The number of haplotypes verified by the total number of haplotypes examined.
GAPPED_ALIGNMENTS_ATTEMPTED: The number of gapped alignments attempted
LOCI_MATCHED_1_CATALOG_LOCUS: The number of loci that matched more than one catalog locus and were excluded.
HAPLOTYPES_VERIFIED_EXAMINED: The number of haplotypes verified by the total number of haplotypes examined.
BLACKLISTED_LOCI_MATCHED_NO_CATALOG: The number of loci blacklisted because of no match with the catalog.
GAPPED_BLACKLISTED_LOCI_MATCHING_MORE_1_CATALOG_LOCUS: The number of loci that matched more than one catalog locus and were excluded.
GAPPED_BLACKLISTED_LOCI_UNACCOUNTED_SNP: The number of loci that contained SNPs unaccounted for in the catalog and were excluded.
LOCI_NO_VERIFIED_HAPLOTYPES: The number of loci with no verified haplotypes.
BLACKLISTED_LOCI_INCONSISTENT_ALIGNMENTS: The number of loci blacklisted because of inconsistent alignments.
TOTAL_SAMPLE_LOCI: This is the number of loci that will be used in stacks tsv2bam.
References
Catchen JM, Amores A, Hohenlohe PA et al. (2011) Stacks: Building and Genotyping Loci De Novo From Short-Read Sequences. G3, 1, 171-182.
Catchen JM, Hohenlohe PA, Bassham S, Amores A, Cresko WA (2013) Stacks: an analysis tool set for population genomics. Molecular Ecology, 22, 3124-3140.
See Also
Examples
1 2 3 4 5 6 7 | ## Not run:
sum <- stackr::summary_sstacks(
sstacks.log = "09_log_files/sstacks_20191101@1108.log",
verbose = TRUE
)
## End(Not run)
|
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