I have the following dataset:
ï..TGEClass.known TGEClass.uknown 1 GVVEVTHDLQK GVVEVTHDLQK 2 LFYADHPFIFLVR LFYADHPFIFLVR 3 SALQSINEWAAQTTDGK SALQSINEWAAQTTDGK 4 AVLSAEQLRDEEVHAGLGELLR AVLSAEQLRDEEVHAGLGELL
I would like to calculate please the number of peptides that are present in both categories and those that are not.
I have tried to use the Venn count function from limma but that only accepts numerical values:
a <- vennCounts(c3) a hw hm hr Counts [1,] 0 0 0 113 [2,] 0 0 1 18 [3,] 0 1 0 8 [4,] 0 1 1 8 [5,] 1 0 0 12 [6,] 1 0 1 8 [7,] 1 1 0 11 [8,] 1 1 1 22
How I can convert my peptide dataset like that dataset above so that I can make a Venn diagram. I have researched everywhere I can but still failed to find the solution.
I would really appreciate it if someone could help me solve this problem.
Hi SMK, Thanks very much for your answer but how can I get a table like this automatically, it is quite long to do it manually?
Sorry those are meant to say TGEClass.uknown and TGEClass known. Please ignore the hw, hm and hr, I want table like that for TGEClass known and TGEClass unknown
Hi SMK thanks a lot thats what was look for. Just one final question if you don't mind.
I have a lot of data frames like the one above but each one has a different number of categories and also different categories, would it be possible to intersect and setdif between all the different columns automatically?
Got an idea from the function:
venn, here demonstrating 2 sets and 3 sets:
Hi SMK, Unfortunately, I found just now that I can't do a Venn diagram for more than 5 categories.
Can you help me create a df that looks like this please?
Thanks very much
Thanks very much for your quick response, I have been trying all day to fix this. You are a life saver!
Hi SMK, sorry for the lateness, is there a way to see the number of unique peptides from each category when there are blanks in columns, please?
length codesees the blank cells as unique peptides, unfortunately.
You can remove the empty element in list before you use
Hi SMK , thank you again for your quick response. Much Appreciated.
Cool, glad it helps!