ri_data_extract | R Documentation |
A convenient function to extract peak data from a RI file. This function is mostly
intended for debugging purposes, for example, when a given peak is not found within
a expected time range (which could be because a faulty retention time correction).
The arguments of this function are similar as those of the ncdf4_data_extract
function.
ri_data_extract(RIfile, massValues, timeRange, useRT = FALSE, ...)
RIfile |
A path to a RI file format (binary or text). |
massValues |
A numeric vector representing m/z values. The values will be converted to integers internally. |
timeRange |
A numeric vector of even length, or, a two-column matrix. This parameter represents the lower and upper time limits. See details below. |
useRT |
Logical. If |
... |
Extra parameters passed to internal functions. Currently, only the |
The function takes a RI file generated by TargetSearch
(binary or text works)
and extracts all the peaks detected of given m/z ion traces in a given time range.
The time range can be in seconds or arbitrary retention time index units.
The parameter timeRange
can be either a numeric vector of even length or a
two-column matrix. If it is a matrix, the first column represent the lower bounds
while the second the upper ones. If it is a vector, it must have at least two elements,
which in this case represent the lower and upper limits, or if longer, it will be coerced to matrix
internally (Important: the values are filled by columns). In any case,
the number of rows of the (coerced) matrix must divide the length of the massValues
parameter, such that each row corresponds to a time range for each m/z value.
This is done so the ranges can be recycled.
The output is simply a four column matrix in which a row is a peak of a given ion trace at a retention time (index). The output is always a matrix even if no peaks are found, in which case the number of rows is zero.
A four column matrix with column names described below. Each row represents a peak in the specified time range. Potentially, there could be zero rows if no peaks are found.
RI
retention time index of the peak.
RT
retention time.
Intensity
peak height intensity
mz
the m/z of the peak
This function is intended to be used internally or by advances users. It can be used
for debugging when TargetSearch
fails to find a peak.
See also the function FindAllPeaks
which offers a similar functionality
but with different input parameters.
Alvaro Cuadros-Inostroza
text2bin
,
ncdf4_data_extract
,
FindAllPeaks
,
FindPeaks
require(TargetSearchData)
path <- tsd_data_path()
rifile <- tsd_rifiles()[1]
# extract peak data for m/z 116 and 117 in time range 180 - 220 seconds
data <- ri_data_extract(rifile, c(116, 117), c(180, 220), useRT=TRUE)
# same but using Retention Time Index
data <- ri_data_extract(rifile, c(116, 117), c(205000, 228000), useRT=FALSE)
# different time ranges for each m/z
trange <- c(180, 240, 280, 190, 250, 290)
data <- ri_data_extract(rifile, c(116, 144, 147), trange, useRT=TRUE)
# Note: the range definition above is equivalent to
trange <- cbind(c(180,240,280), c(190, 250, 290))
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.