Description Usage Arguments Details Value See Also Examples
A wrapper function for applying cubic spline drift correction and saving before and after plots
1 2 3 4 5 |
object |
a MetaboSet object |
spar |
smoothing parameter |
spar_lower, spar_upper |
lower and upper limits for the smoothing parameter |
condition |
a character specifying the condition used to decide whether drift correction works adequately, see Details |
plotting |
logical, whether plots should be drawn |
file |
path to the PDF file where the plots should be saved |
width, height |
width and height of the plots in inches |
color |
character, name of the column used for coloring the points |
shape |
character, name of the column used for shape |
color_scale |
the color scale as returned by a ggplot function |
If spar
is set to NULL
(the default), the smoothing parameter will
be separately chosen for each feature from the range [spar_lower, spar_upper
]
using cross validation. The condition
parameter should be a character giving a condition compatible
with dplyr::filter. The condition is applied on the changes in the quality metrics
RSD, RSD_r, D_ratio and D_ratio_r. For example, the default is "RSD_r < 0 and D_ratio_r < 0",
meaning that both RSD_r and D_ratio_r need to decrease in the drift correction, otherwise the
drift corrected feature is discarded and the original is retained. If shape
is set to NULL
(the default), the column used for color
is also used for shape
MetaboSet object as the one supplied, with drift corrected features
dc_cubic_spline
, smooth.spline
for details about the regression,
inspect_dc
for analysing the drift correction results,
save_dc_plots
for plotting the drift correction process for each feature
1 | corrected <- correct_drift(merged_sample)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.