I have also tried the following to receive this error:

ConALL

'filter' in dplyr applies to rows, meaning you filter out or in some rows meeting the requirement in the 'filter' clause.

Now I see that Con1 is a column in your dataframe, so the function to call is "select".

To exclude it you can try

new_df = fm %>%

dplyr::select(-Con1)

You may want to read about dplyr operators before you apply it.

https://cran.r-project.org/web/packages/dplyr/vignettes/dplyr.html

Ginny Xiaohe Li Thank you very much for your comment!

I had a look at the link sent and I believe filter would be the right function as I want to filter out rows in reference to Con1 rather than to remove columns. Perhaps a better way for me to explain this is by showing an edited image of what I would like to achieve. The following image shows the rows "cysI" and "cysj" filtered out from fm as they are found in Con1 to achieve the final matrix I want. Of course this would not be possible manually as I have a list of over 4000 genes.

https://imgur.com/cMsTfGo

I have however also gone ahead to try the solution you proposed anyways to receive the following error:

ConAll % dplyr::select(-Con1)

Error: Must subset columns with a valid subscript vector. x Subscript has the wrong type `data.frame`. i It must be numeric or character.

I tried filter in the function you suggested to get this error:

ConAll % dplyr::filter(-Con1)

Error: Problem with `filter()` input `..1`. x invalid argument to unary operator i Input `..1` is `-Con1`.

Pardon if I got the idea of using filter wrong still and please correct me if im wrong again!

got what you mean.

So apparently this involves two dataframes.

I suggest you to assign a column name to the genes (first column) in the first dataframe fm, lets say name it with 'Gene', then you want to find out the set of genes you want to keep there.

say, genes_keep = setdiff(fm$Gene, Con1) #### ones in fm but not in Con1

then you go with filter.

new_fm = fm %>%

dplyr::filter(Gene %in% genes_keep)

Ginny Xiaohe Li

Thank you very much for this solution! After tweaking some of the variables I was able to get it to work!

inner_join(), left_join(), right_join() functions in "dplyr" package are also useful to match or exclude rows in two data frames

This link may be useful

https://dplyr.tidyverse.org/reference/join.html

You can equate the intended rows, columns, or entries to a null array. It works for you.