5.22 groupBy

groupBy is a useful tool that mimics the “groupBy” clause in database systems. Given a file or stream that is sorted by the appropriate “grouping columns”, groupBy will compute summary statistics on another column in the file or stream. This will work with output from all BEDTools as well as any other tab-delimited file or stream.

NOTE: When using groupBy, the input data must be ordered by the same columns as specified with the -grp argument. For example, if -grp is 1,2,3, the the data should be pre-grouped accordingly. When groupBy detects changes in the group columns it then summarizes all lines with that group.

5.22.1 Usage and option summary

Usage:

groupBy [OPTIONS] -i <input> -opCol <input column>

Option	Description
-i	The input file that should be grouped and summarized. Use “stdin” when using piped input. Note: if -i is omitted, input is assumed to come from standard input (stdin)
-g OR -grp	Specifies which column(s) (1-based) should be used to group the input. The columns must be comma-separated and each column must be explicitly listed. No ranges (e.g. 1-4) yet allowed. Default: 1,2,3
-c OR -opCol	Specify the column (1-based) that should be summarized. Required.
-o OR -op	Specify the operation that should be applied to opCol. Valid operations: sum - numeric only count - numeric or text min - numeric only max - numeric only mean - numeric only stdev - numeric only median - numeric only mode - numeric or text antimode - numeric or text collapse (i.e., print a comma separated list) - numeric or text freqasc - print a comma separated list of values observed and the number of times they were observed. Reported in ascending order of frequency freqdesc - print a comma separated list of values observed and the number of times they were observed. Reported in descending order of frequency Default: sum

5.22.2 Default behavior.

Let’s imagine we have three incredibly interesting genetic variants that we are studying and we are interested in what annotated repeats these variants overlap.

cat variants.bed
chr21  9719758 9729320 variant1
chr21  9729310 9757478 variant2
chr21  9795588 9796685 variant3

intersectBed -a variants.bed -b repeats.bed -wa -wb > variantsToRepeats.bed
cat variantsToRepeats.bed
chr21  9719758 9729320 variant1   chr21  9719768 9721892 ALR/Alpha   1004  +
chr21  9719758 9729320 variant1   chr21  9721905 9725582 ALR/Alpha   1010  +
chr21  9719758 9729320 variant1   chr21  9725582 9725977 L1PA3       3288  +
chr21  9719758 9729320 variant1   chr21  9726021 9729309 ALR/Alpha   1051  +
chr21  9729310 9757478 variant2   chr21  9729320 9729809 L1PA3       3897  -
chr21  9729310 9757478 variant2   chr21  9729809 9730866 L1P1        8367  +
chr21  9729310 9757478 variant2   chr21  9730866 9734026 ALR/Alpha   1036  -
chr21  9729310 9757478 variant2   chr21  9734037 9757471 ALR/Alpha   1182  -
chr21  9795588 9796685 variant3   chr21  9795589 9795713 (GAATG)n    308   +
chr21  9795588 9796685 variant3   chr21  9795736 9795894 (GAATG)n    683   +
chr21  9795588 9796685 variant3   chr21  9795911 9796007 (GAATG)n    345   +
chr21  9795588 9796685 variant3   chr21  9796028 9796187 (GAATG)n    756   +
chr21  9795588 9796685 variant3   chr21  9796202 9796615 (GAATG)n    891   +
chr21  9795588 9796685 variant3   chr21  9796637 9796824 (GAATG)n    621   +

We can see that variant1 overlaps with 3 repeats, variant2 with 4 and variant3 with 6. We can use groupBy to summarize the hits for each variant in several useful ways. The default behavior is to compute the sum of the opCol.

groupBy -i variantsToRepeats.bed -grp 1,2,3 -opCol 9
chr21 9719758 9729320 6353
chr21 9729310 9757478 14482
chr21 9795588 9796685 3604

5.22.3 Computing the min and max.

Now let’s find the min and max repeat score for each variant. We do this by “grouping” on the variant coordinate columns (i.e. cols. 1,2 and 3) and ask for the min and max of the repeat score column (i.e. col. 9).

groupBy -i variantsToRepeats.bed -g 1,2,3 -c 9 -o min
chr21 9719758 9729320 1004
chr21 9729310 9757478 1036
chr21 9795588 9796685 308

We can also group on just the name column with similar effect.

groupBy -i variantsToRepeats.bed -grp 4 -opCol 9 -op min
variant1 1004
variant2 1036
variant3 308

What about the max score? Let’s keep the coordinates and the name of the variants so that we stay in BED format.

groupBy -i variantsToRepeats.bed -grp 1,2,3,4 -opCol 9 -op max
chr21 9719758 9729320 variant1 3288
chr21 9729310 9757478 variant2 8367
chr21 9795588 9796685 variant3 891

5.22.4 Computing the mean and median.

Now let’s find the mean and median repeat score for each variant.

cat variantsToRepeats.bed | groupBy -g 1,2,3,4 -c 9 -o mean
chr21 9719758 9729320 variant1 1588.25
chr21 9729310 9757478 variant2 3620.5
chr21 9795588 9796685 variant3 600.6667

groupBy -i variantsToRepeats.bed -grp 1,2,3,4 -opCol 9 -op median
chr21 9719758 9729320 variant1 1030.5
chr21 9729310 9757478 variant2 2539.5
chr21 9795588 9796685 variant3 652

5.22.5 Computing the mode and “antimode”.

Now let’s find the mode and antimode (i.e., the least frequent) repeat score for each variant (in this case they are identical).

groupBy -i variantsToRepeats.bed -grp 1,2,3,4 -opCol 9 -op mode
chr21 9719758 9729320 variant1 1004
chr21 9729310 9757478 variant2 1036
chr21 9795588 9796685 variant3 308

groupBy -i variantsToRepeats.bed -grp 1,2,3,4 -opCol 9 -op antimode
chr21 9719758 9729320 variant1 1004
chr21 9729310 9757478 variant2 1036
chr21 9795588 9796685 variant3 308

5.22.6 Computing the count of lines for a given group.

Figure:

groupBy -i variantsToRepeats.bed -g 1,2,3,4 -c 9 -c count
chr21 9719758 9729320 variant1 4
chr21 9729310 9757478 variant2 4
chr21 9795588 9796685 variant3 6

5.22.7 Collapsing: listing all of the values in the opCol for a given group.

Now for something different. What if we wanted all of the names of the repeats listed on the same line as the variants? Use the collapse option. This “denormalizes” things. Now you have a list of all the repeats on a single line.

groupBy -i variantsToRepeats.bed -grp 1,2,3,4 -opCol 9 -op collapse
chr21 9719758 9729320 variant1 ALR/Alpha,ALR/Alpha,L1PA3,ALR/Alpha,
chr21 9729310 9757478 variant2 L1PA3,L1P1,ALR/Alpha,ALR/Alpha,
chr21 9795588 9796685 variant3 (GAATG)n,(GAATG)n,(GAATG)n,(GAATG)n,(GAATG)n,(GAATG)n,

5.22.8 Computing frequencies: freqasc and freqdesc.

Now for something different. What if we wanted all of the names of the repeats listed on the same line as the variants? Use the collapse option. This “denormalizes” things. Now you have a list of all the repeats on a single line.

cat variantsToRepeats.bed | groupBy -g 1 -c 8 -o freqdesc
chr21 (GAATG)n:6,ALR/Alpha:5,L1PA3:2,L1P1:1,

cat variantsToRepeats.bed | groupBy -g 1 -c 8 -o freqasc
chr21 L1P1:1,L1PA3:2,ALR/Alpha:5,(GAATG)n:6,