matrixStats | R package : Methods that Apply to Rows and Columns | Build Tool library

I have a function that I need to run on 2000 data frames. Each iteration is taking a very long time i.e almost 40 minutes and hence I'm using the 'foreach' package in R. I have generated the data in the following way:

I want to create a function which helps characterise the results to some simulations. For the purposes of this post let the simulation function be:

I have downloaded Proteome Profiling data from the TCGA-LGG project with the Bioconductor package TCGAbiolinks. Then I have the following error when running GDCprepare:

I have a matrix and would like to do the following:

1. Remove all rows containing "Z" more than once
2. Remove all rows containing at least two occurrences of "S" in direct neighbor columns
3. Remove all rows in which "2D" exists not only once and in which "1D" is not or not only once being present in a more left column (lower column number)

Here is a MWE with explanation:

I'm trying to calculate the 1st and 3rd quartiles for each row in my data frame and save them as new columns. I tried using matrixStats::rowQuantiles, but it gives an NA value for the row containing NAs even though I set na.rm=TRUE to remove NAs before calculating.

I also noticed that the values for Q1 and Q3 are the same for each row. It's more likely that I'm using the function wrong than that these are actually the same, but I can't figure out what I'm doing wrong.

Thanks in advance!

It is a very simple task to replace NAs with medians by column. But how to replace NA values with a row median? I tried matrixStats::rowMedians and it does not work.

Sample:

I'm observing a very strange behaviour with R.

The following code works when I type it in line-by-line into an instance of R run from my terminal. (OS is Debian Linux.)

However it does not work when I try and run source("script.R").

It also does not work from within R Studio.

Specifically, it fails to produce graphical output with autoplot. Writing to pdf file does not work, and if I remove the pdf() and dev.off() lines, no window containing the figure is opened.

Here's a copy of my script...

I'm confused by the coefficients produced by the output of lm

Here's a copy of the data I'm working with

hope someone can help with this one:

My code below was returning a dinamic table as I intend, but when I created the for loop to assign individually random numbers to each [k,p] position in the table all the calculations stop and I see an empty UI.

If instead of
rv$MCProbTable[[k,p]] = round(as.numeric(stats::runif(1,0,100)), 3)
I use for example
rv$MCProbTable[[k,p]] = 2
I see "2" allocated in each position in the table, what is close to what I want and shows that everything is working up to the runif application. So is it an issue with the function? Or most likely it is the reactive for loop that isn't set properly?

Thanks and hope this is an easy one!