heidel

This packages is just some random functions that are used for very specific tasks during my study. It is only to share with collaborators and between workstations.

Installation

Install package using devtools

if(!require("devtools")) install.packages("devtools")
library(devtools)
devtools::install_github("SorenHeidelbach/miscR")

Usage examples

count_unique

library(miscR)

counted = count_unique(iris, 
                       subset_by = "Species", 
                       count_col = 1)
head(counted)
#>   Sepal.Length setosa versicolor virginica
#> 1          4.9      1          1         4
#> 2          5.6      1          5         0
#> 3          5.7      1          5         2
#> 4          5.8      3          3         1
#> 5          5.9      1          2         0
#> 6            6      2          4         0
species <- iris$Species[c(1,60)]
counted = count_unique(iris, 
                       subset_by = "Species", 
                       count_col = "Sepal.Length",
                       subset_values = species)
head(counted)
#>   Sepal.Length setosa versicolor
#> 1          4.9      1          4
#> 2            5      2          8
#> 3          5.1      1          8
#> 4          5.2      1          3
#> 5          5.4      1          5
#> 6          5.5      5          2

tax_lineage_from_accesion

tax_lineage_from_accesion(accession = c("NZ_CP027599.1", "NR_042763"))
#>           rank       NZ_CP027599.1           NR_042763
#> 8 superkingdom            Bacteria            Bacteria
#> 4      kingdom                <NA>                <NA>
#> 6       phylum      Proteobacteria      Proteobacteria
#> 1        class Gammaproteobacteria Alphaproteobacteria
#> 5        order    Enterobacterales    Rhodospirillales
#> 2       family  Enterobacteriaceae    Acetobacteraceae
#> 3        genus         Escherichia    Komagataeibacter
#> 7      species                coli           rhaeticus

tax_lineage_from_accesion(accession = c("NZ_CP027599.1", "7"),
                          custom_tax = c("clade", "genus", "species"))
#>       rank NZ_CP027599.1            7
#> 1    clade          <NA> Opisthokonta
#> 15   genus   Escherichia          Bos
#> 16 species          coli       taurus

evaluate_contig_coverage

# Some large contigs have been removed from depth file to reduce file size.
evaluate_contig_coverage(path = "depth.AF1_seqtk.filt.txt", 
                         parametric = T) 

evaluate_contig_coverage(path = "depth.AF1_seqtk.filt.txt", 
                         parametric = F)