Description Usage Arguments Details Value Examples
Filters mass spectrometry data using a set of criteria, described in
Details
. Returns an object of classes msDat
and
filterMS
.
1 2 | filterMS(msObj, region, border = "all", bord_ratio = 0.05,
min_inten = 1000, max_chg = 7L)
|
msObj |
An object class |
region |
A vector either of mode character or mode numeric. If numeric
then the entries should provide the indices for the region of interest in
the mass spectrometry data provided as the argument for |
border |
Either a character string |
bord_ratio |
A single nonnegative numeric value. A value of 0 will not admit any compounds, while a value greater than 1 will admit all compounds (see criterion 2). |
min_inten |
A single numeric value. A value less than the minimum mass spectrometry value in the data will admit all compounds (see criterion 4). |
max_chg |
A single numeric value specifying the maximum charge which a compound may exhibit (see criterion 5) |
Attempts to filter out candidate compounds via subject-matter knowledge, with the goal of removing spurious noise from downstream models. The criteria for the downstream inclusion of a candidate compound is listed below.
The m/z intensity maximum must fall inside the range of the bioactivity region of interest
The ratio of the m/z intensity of a species in the areas bordering
the region of interest and the species maximum intensity must be less
than bord_ratio
. When there is no bordering area then it is
taken to mean that all observations satisfy this criterion.
The immediately right adjacent fraction to its maximum intensity fraction for a species must have a non-zero abundance. In the case of ties for the maximum, it is the fraction immediately to the right of the rightmost maximum fraction which cannot have zero abundance. When the fraction with maximum intensity is the rightmost fraction in the data for an observation, then it is taken to mean that the observation satisfies this criterion.
At least 1 fraction in the region of interest must have intensity
greater than min_inten
Compound charge state must be less than or equal to max_chg
Returns an object of class filterMS
which inherits from
msDat
. This object is a list
with elements described
below. The class is equipped with a print
, summary
, and
extractMS
function.
msDatObj
An object of class msDat
such that
the encapsulated mass spectrometry data corresponds to each of the
candidate compounds that satisfed each of the criteria. If no
criteria are satisfied then NULL
is returned.
cmp_by_crit
A list containing data.frame
s, one for
each criterion. Each row (if any) in one of the
sub-data.frame
s contains the mass-to-charge and charge
information for a candidate compound that satisfies the criterion
represented by the data.frame
; all of the compounds that
satisfied the criterion are included in the data. The
data.frame
s are named c1
, ..., c5
, etc
corresponding to criterion 1, ..., criterion 5.
summ_info
A list containing information pertaining to the filtering process; for use by the summary function.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 | # Load mass spectrometry data
data(mass_spec)
# Convert mass_spec from a data.frame to an msDat object
ms <- msDat(mass_spec = mass_spec,
mtoz = "m/z",
charge = "Charge",
ms_inten = c(paste0("_", 11:43), "_47"))
# Filter out potential candidate compounds
filter_out <- filterMS(msObj = ms,
region = paste0("VO_", 17:25),
border = "all",
bord_ratio = 0.01,
min_inten = 1000,
max_chg = 7)
# print, summary function
filter_out
summary(filter_out)
# Extract filtered mass spectrometry data as a matrix or msDat object
filter_matr <- extractMS(msObj = filter_out, type = "matrix")
filter_msDat <- extractMS(msObj = filter_out, type = "matrix")
|
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