To combine more than one MaxQuant file, you can use the
load_multiple_maxquant() function to load them all into
R.
The best approach is to place each proteinGroups.txt
into its own subdirectory in the Data directory; the
command will find and load any proteinGroups.txt in the
Data directory.
The output of load_multiple_maxquant() is a list of data
frames containing the combined data from all the files.
Processing the data
Specifiying groups
Using process_multiple_maxquant() with the list of data
frames, you will be given the option of specifying which group(s)
corresponds to group1 (right side of the volcano plot) and which
group(s) corresponds to group2 (left side of the volcano plot). The
function will then combine the data from all the files and return a
single data frame that can be used for plotting.
In a simple example, two MaxQuant files have two groups each, “WT” and “Control”. The runs in the both files are called WT.1, WT.2, WT.3, Control.1, Control.2, Control.3. The function presents the user with a list of the groups found in the files and asks which group(s) should be used for group1 and which group(s) should be used for group2. If we specify WT as group1 and Control as group2, the function will combine them. In doing so it will rename the runs to test.1, test.2, test.3, test.4, test5, test.6, control.1, control.2, control.3, control.4, control.5, control.6 to avoid any duplicate names.
In a more complicated example, in another set, the groups are called “WT” and “Control” in one file and “wildtype” and “control” in the other. The user can select from a list to specify the groups in group1 and those in group2. They would see a list of 1 WT, 2 Control, 3 wildtype, 4 control. If they select “1 3” for group1 and “2 4” for group2, the function will combine them and rename the runs to test.1, test.2, test.3, test.4, test5, test.6, control.1, control.2, control.3, control.4, control.5, control.6.
Note that the group names need to be unique and logical, for example if WT and Control are mislabelled in one file, or if names are shared between those in group1 and group2 then they cannot be combined. The solution here is to rerun MaxQuant with appropriate labelling.
In both of these examples, the user can bypass the selection step by
specifying the groups in the function call, that is using
load_multiple_maxquant(group1 = "WT", group2 = "Control")
for the first example and
load_multiple_maxquant(group1 = c("WT", "wildtype"), group2 = c("Control", "control"))
for the second example.
library(VolcanoPlotR)
my_list <- load_multiple_maxquant()
df_subset <- process_multiple_maxquant(data = my_list)
# or to bypass the selection step, specify the groups in the function call
df_subset <- process_multiple_maxquant(data = my_list, group1 = c("WT", "wildtype"), group2 = c("Control", "control"))There is an additional argument that can be used to use the average
of the ratios rather than ratio the averages. This is useful if datasets
have been combined but they have differing intensities. Using
ratio = TRUE will compare test.1 with control.1, test.2
with control.2, etc. and then average the ratios. Using
ratio = FALSE will average the test samples and average the
control samples and then compare the averages (this is the only option
in the single file case). The default is ratio = FALSE.
Plotting
The next steps are the same as if a single MaxQuant file had been
used. Use volcano_plot_maxquant() or
pca_plot_maxquant() or mean_plot_maximum() to
generate the plots. process_multiple_maxquant() can be used
as input to either of these functions.