jd_rds: Merge ASV sequence tables (RDS files) from DADA2 and annotate...
In jdwiyanto/mbiome: A convenient wrapper to visualise and run core analyses for multi-variable microbiome data
Description
Usage
Arguments
Value
Description
Function must be run on main folder containing all seqtab.RDS files to be annotated (recursive folders supported).
This function will output abundance and taxonomy tables in the working directory.
Usage
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jd_rds(
seqlength_min = 400,
seqlength_max = 470,
refpath = "E:/ubuntu/virtual_shared/silva_nr99_v138_wSpecies_train_set.fa.gz"
)
Arguments
seqlength_min
minimum sequence length to keep, default to 400 for V3-V4 region
seqlength_max
maximum sequence length to keep, default to 470 for V3-V4 region
refpath
path to SILVA reference database
Value
csv files of abundance and taxonomy table
jdwiyanto/mbiome documentation built on April 18, 2021, 3:31 a.m.
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Description Usage Arguments Value
Description
Function must be run on main folder containing all seqtab.RDS files to be annotated (recursive folders supported). This function will output abundance and taxonomy tables in the working directory.
Usage
1 2 3 4 5 | jd_rds(
seqlength_min = 400,
seqlength_max = 470,
refpath = "E:/ubuntu/virtual_shared/silva_nr99_v138_wSpecies_train_set.fa.gz"
)
|
Arguments
seqlength_min |
minimum sequence length to keep, default to 400 for V3-V4 region |
seqlength_max |
maximum sequence length to keep, default to 470 for V3-V4 region |
refpath |
path to SILVA reference database |
Value
csv files of abundance and taxonomy table
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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