Hi Guys, I'm having trouble with some data manipulation. I have the following table where I have the raw counts from an RNA-seq experiment. I'm trying to group all my counts by tRNA wobble position.
head(df)
Isodecoder Anticodon Wobble Loci Fragment_type AAV_Ctrl1 AAV_Ctrl2 AAV_Ctrl3 AAV_Cre1 AAV_Cre2 AAV_Cre3
Ala AGC A 1 wholecounts 8 3 0 35 58 61
Ala AGC A 10 wholecounts 0 0 0 0 2 0
Ala AGC A 12 wholecounts 0 0 0 0 0 0
Ala AGC A 2 wholecounts 1228 839 766 1115 1525 784
Ala AGC A 3 wholecounts 286 125 120 504 387 380
Ala AGC A 4 wholecounts 675 541 353 328 452 367
I'm essentially trying to sum counts by Isodecoder and wobble position (i.e for Ala, I'd have 1 value for wobble A, T, C and G for each of my conditions Ctrl1-3 and Cre1-3). Tried to use dplyr with no luck. THANKS IN ADVANCE!!!
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1 answer
You can use aggregate through base R to accomplish this if you're just trying to sum by Isodecoder.
> df.agg <- aggregate(df[,-seq(5)],list(df$Isodecoder),sum)
> df.agg
Group.1 AAV_Ctrl1 AAV_Ctrl2 AAV_Ctrl3 AAV_Cre1 AAV_Cre2 AAV_Cre3
1 Ala 2197 1508 1239 1982 2424 1592
The above command is making a new data frame called df.agg by taking all of the counts in df (removing the first five columns), aggregating it based on the values in df$Isodecoder, and performing the sum function.
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Could you show your dplyr attempt, please