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Filter Features based on their mass-to-charge ratios

Source: R/filters.R
filter_mz.Rd

Facilitates filtering by given mass-to-charge ratios (m/z) with a defined tolerance. Can also be used to filter based on exact mass.

Usage

filter_mz(data, m_z_col, masses, tolerance = 5, tolerance_type = "ppm")

Arguments

data

A tidy tibble created by read_featuretable.

m_z_col

Which column holds the precursor m/z (or exact mass)? Uses args_data_masking.

masses

The mass(es) to filter by.

tolerance

A numeric. The tolerance to apply to the masses Either an absolute value in Da (if tolerance_type = "absolute") or in ppm (if tolerance_type = "ppm").

tolerance_type

Either "absolute" or "ppm". Should the tolerance be an absolute value or in ppm?

Value

A filtered tibble.

Examples

# Use a tolerance of plus or minus 5 ppm
toy_metaboscape %>%
  filter_mz(m_z_col = `m/z`, 162.1132, tolerance = 5, tolerance_type = "ppm")
#> # A tibble: 11 × 8
#>      UID Feature              Sample  Intensity    RT `m/z` Name  Formula 
#>    <int> <chr>                <chr>       <dbl> <dbl> <dbl> <chr> <chr>   
#>  1     1 161.10519 Da 26.98 s Sample1         4  0.45  162. NA    C7H15NO3
#>  2     1 161.10519 Da 26.98 s Sample2         3  0.45  162. NA    C7H15NO3
#>  3     1 161.10519 Da 26.98 s Sample3         4  0.45  162. NA    C7H15NO3
#>  4     1 161.10519 Da 26.98 s Sample4        NA  0.45  162. NA    C7H15NO3
#>  5     1 161.10519 Da 26.98 s Sample5         9  0.45  162. NA    C7H15NO3
#>  6     1 161.10519 Da 26.98 s Sample6         8  0.45  162. NA    C7H15NO3
#>  7     1 161.10519 Da 26.98 s QC1             7  0.45  162. NA    C7H15NO3
#>  8     1 161.10519 Da 26.98 s QC2             6  0.45  162. NA    C7H15NO3
#>  9     1 161.10519 Da 26.98 s QC3             3  0.45  162. NA    C7H15NO3
#> 10     1 161.10519 Da 26.98 s Blank1         NA  0.45  162. NA    C7H15NO3
#> 11     1 161.10519 Da 26.98 s Blank2         NA  0.45  162. NA    C7H15NO3

# Use a tolerance of plus or minus 0.005 Da
toy_metaboscape %>%
  filter_mz(m_z_col = `m/z`, 162.1132, tolerance = 0.005, tolerance_type = "absolute")
#> # A tibble: 11 × 8
#>      UID Feature              Sample  Intensity    RT `m/z` Name  Formula 
#>    <int> <chr>                <chr>       <dbl> <dbl> <dbl> <chr> <chr>   
#>  1     1 161.10519 Da 26.98 s Sample1         4  0.45  162. NA    C7H15NO3
#>  2     1 161.10519 Da 26.98 s Sample2         3  0.45  162. NA    C7H15NO3
#>  3     1 161.10519 Da 26.98 s Sample3         4  0.45  162. NA    C7H15NO3
#>  4     1 161.10519 Da 26.98 s Sample4        NA  0.45  162. NA    C7H15NO3
#>  5     1 161.10519 Da 26.98 s Sample5         9  0.45  162. NA    C7H15NO3
#>  6     1 161.10519 Da 26.98 s Sample6         8  0.45  162. NA    C7H15NO3
#>  7     1 161.10519 Da 26.98 s QC1             7  0.45  162. NA    C7H15NO3
#>  8     1 161.10519 Da 26.98 s QC2             6  0.45  162. NA    C7H15NO3
#>  9     1 161.10519 Da 26.98 s QC3             3  0.45  162. NA    C7H15NO3
#> 10     1 161.10519 Da 26.98 s Blank1         NA  0.45  162. NA    C7H15NO3
#> 11     1 161.10519 Da 26.98 s Blank2         NA  0.45  162. NA    C7H15NO3