Description Usage Arguments Details Value Author(s) Examples
Calculates some basic statistics like the N50 length, minimum-, mean-, and maximum scaffold lengths, mean GC content, information about essential genes, and more...
1 |
mm |
(required) A dataframe loaded with |
original_data |
If |
print |
(logical) Whether to print the calculated stats or not. (Default: |
The returned stats are calculated as follows:
Scaffolds: The number of different scaffolds in the assembly.
N50: The shortest sequence length at 50
Length.total: The total size of the assembly.
Length.max: The size of the largest scaffold in the assembly.
Length.mean: The average scaffold size in the assembly.
Length.min: The size of the smallest scaffold in the assembly.
weighted_GC_mean: The average GC content in the assembly, weighted by scaffold sizes.
cov_*: The average coverage of each coverage variable in mm, weighted by scaffold sizes. (Only columns starting with "cov_" will be shown)
Ess.genes.total: The total number of essential genes, if any have been loaded.
Ess.genes.unique: The number of unique essential genes, if any have been loaded.
A dataframe with the calculated stats is returned invisibly.
Kasper Skytte Andersen ksa@bio.aau.dk
Soren M. Karst smk@bio.aau.dk
Mads Albertsen MadsAlbertsen85@gmail.com
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | library(mmgenome2)
data(mmgenome2)
mmstats(mmgenome2)
# Compare an extraction with the original data from which the extraction originates:
selection <- data.frame(
cov_C13.11.25 = c(7.2, 16.2, 25.2, 23.3, 10.1),
cov_C14.01.09 = c(47, 77, 52.8, 29.5, 22.1)
)
mmgenome2_extraction <- mmextract(mmgenome2,
selection = selection
)
mmstats(mmgenome2_extraction, original_data = mmgenome2)
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