events() Issue: Error in aggregate.formula

[manojbhagwat123]

Hi,

I am trying to adapt the "Classifying SV events" part of the gGnome tutorial to my own generated jabba.rds files.

I am running R version 4.3.1, for which I installed the gGnome package.

This is the code I used to try to generate the events():

library(gGnome)
jabba <- readRDS('/path/to/jabba.rds')
gg <- gG(jabba = jabba)
gg <- events(gg, verbose = TRUE)
saveRDS(gg, file = '/path/to/jabba_events.rds')

Running this above code gave the following in my console:

Finished simple
Finished amp (Tyfonas, dm, cmxdm, bfb)
Finished chromothrpisis
Finished del
Loading required package: MASS
Error in aggregate.formula(formula = subject.id ~ grl.id, data = m, FUN = function(x) numwin -  : 
  argument 'x' is  missing -- it has been renamed from 'formula'
In addition: There were 19 warnings (use warnings() to see them)

It seems that this error occurs after "Loading required package: MASS", following the del classification step completing.

I tried this with my respective jabba.gg.rds instead of jabba.rds, and that did not fix the issue either.

I was wondering how I could go about solving this issue; please let me know. Thank you.

If helpful at all, here are the 19 warnings via running warnings():

Warning messages:
1: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 9 out-of-bound ranges located on sequences 10,
  14, 21, 4, 5, and 8. Note that ranges located on a sequence whose
  length is unknown (NA) or on a circular sequence are not considered
  out-of-bound (use seqlengths() and isCircular() to get the lengths and
  circularity flags of the underlying sequences). You can use trim() to
  trim these ranges. See ?trim,GenomicRanges-method for more
  information.
2: In gr.findoverlaps(query, target, scol = by, verbose = verbose,  ... :
  findOverlaps applied to ranges with non-identical seqlengths
3: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 3 out-of-bound ranges located on sequences 10,
  14, and 5. Note that ranges located on a sequence whose length is
  unknown (NA) or on a circular sequence are not considered out-of-bound
  (use seqlengths() and isCircular() to get the lengths and circularity
  flags of the underlying sequences). You can use trim() to trim these
  ranges. See ?trim,GenomicRanges-method for more information.
4: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 104 out-of-bound ranges located on sequences 1,
  10, 12, 13, 14, 16, 19, 20, 21, 3, 4, 5, 6, 7, 9, 11, 15, 17, 18, 2,
  22, 8, GL000191.1, GL000192.1, GL000193.1, GL000194.1, GL000195.1,
  GL000196.1, GL000197.1, GL000198.1, GL000199.1, GL000200.1, GL000201.1,
  GL000202.1, GL000203.1, GL000204.1, GL000205.1, GL000206.1, GL000207.1,
  GL000208.1, GL000209.1, GL000210.1, GL000211.1, GL000212.1, GL000213.1,
  GL000214.1, GL000215.1, GL000216.1, GL000217.1, GL000218.1, GL000219.1,
  GL000220.1, GL000221.1, GL000222.1, GL000223.1, GL000224.1, GL000225.1,
  GL000226.1, GL000227.1, GL000228.1, GL000229.1, GL000230.1, GL000231.1,
  GL000232.1, GL000233.1, GL000234.1, GL000235.1, GL000236.1, GL000237.1,
  GL000238.1, GL000239.1, GL000240.1, GL000241.1, GL000242.1, GL000243.1,
  GL000244.1, GL000245.1, GL000246.1, GL000247.1, GL000248.1, GL000249.1,
  MT, X, and Y. Note that ranges located on a sequence whose length is
  unknown (NA) or on a circular sequence are not co [... truncated]
5: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 104 out-of-bound ranges located on sequences 1,
  10, 12, 13, 14, 16, 19, 20, 21, 3, 4, 5, 6, 7, 9, 11, 15, 17, 18, 2,
  22, 8, GL000191.1, GL000192.1, GL000193.1, GL000194.1, GL000195.1,
  GL000196.1, GL000197.1, GL000198.1, GL000199.1, GL000200.1, GL000201.1,
  GL000202.1, GL000203.1, GL000204.1, GL000205.1, GL000206.1, GL000207.1,
  GL000208.1, GL000209.1, GL000210.1, GL000211.1, GL000212.1, GL000213.1,
  GL000214.1, GL000215.1, GL000216.1, GL000217.1, GL000218.1, GL000219.1,
  GL000220.1, GL000221.1, GL000222.1, GL000223.1, GL000224.1, GL000225.1,
  GL000226.1, GL000227.1, GL000228.1, GL000229.1, GL000230.1, GL000231.1,
  GL000232.1, GL000233.1, GL000234.1, GL000235.1, GL000236.1, GL000237.1,
  GL000238.1, GL000239.1, GL000240.1, GL000241.1, GL000242.1, GL000243.1,
  GL000244.1, GL000245.1, GL000246.1, GL000247.1, GL000248.1, GL000249.1,
  MT, X, and Y. Note that ranges located on a sequence whose length is
  unknown (NA) or on a circular sequence are not co [... truncated]
6: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 104 out-of-bound ranges located on sequences 1,
  10, 12, 13, 14, 16, 19, 20, 21, 3, 4, 5, 6, 7, 9, 11, 15, 17, 18, 2,
  22, 8, GL000191.1, GL000192.1, GL000193.1, GL000194.1, GL000195.1,
  GL000196.1, GL000197.1, GL000198.1, GL000199.1, GL000200.1, GL000201.1,
  GL000202.1, GL000203.1, GL000204.1, GL000205.1, GL000206.1, GL000207.1,
  GL000208.1, GL000209.1, GL000210.1, GL000211.1, GL000212.1, GL000213.1,
  GL000214.1, GL000215.1, GL000216.1, GL000217.1, GL000218.1, GL000219.1,
  GL000220.1, GL000221.1, GL000222.1, GL000223.1, GL000224.1, GL000225.1,
  GL000226.1, GL000227.1, GL000228.1, GL000229.1, GL000230.1, GL000231.1,
  GL000232.1, GL000233.1, GL000234.1, GL000235.1, GL000236.1, GL000237.1,
  GL000238.1, GL000239.1, GL000240.1, GL000241.1, GL000242.1, GL000243.1,
  GL000244.1, GL000245.1, GL000246.1, GL000247.1, GL000248.1, GL000249.1,
  MT, X, and Y. Note that ranges located on a sequence whose length is
  unknown (NA) or on a circular sequence are not co [... truncated]
7: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 104 out-of-bound ranges located on sequences 1,
  10, 12, 13, 14, 16, 19, 20, 21, 3, 4, 5, 6, 7, 9, 11, 15, 17, 18, 2,
  22, 8, GL000191.1, GL000192.1, GL000193.1, GL000194.1, GL000195.1,
  GL000196.1, GL000197.1, GL000198.1, GL000199.1, GL000200.1, GL000201.1,
  GL000202.1, GL000203.1, GL000204.1, GL000205.1, GL000206.1, GL000207.1,
  GL000208.1, GL000209.1, GL000210.1, GL000211.1, GL000212.1, GL000213.1,
  GL000214.1, GL000215.1, GL000216.1, GL000217.1, GL000218.1, GL000219.1,
  GL000220.1, GL000221.1, GL000222.1, GL000223.1, GL000224.1, GL000225.1,
  GL000226.1, GL000227.1, GL000228.1, GL000229.1, GL000230.1, GL000231.1,
  GL000232.1, GL000233.1, GL000234.1, GL000235.1, GL000236.1, GL000237.1,
  GL000238.1, GL000239.1, GL000240.1, GL000241.1, GL000242.1, GL000243.1,
  GL000244.1, GL000245.1, GL000246.1, GL000247.1, GL000248.1, GL000249.1,
  MT, X, and Y. Note that ranges located on a sequence whose length is
  unknown (NA) or on a circular sequence are not co [... truncated]
8: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 104 out-of-bound ranges located on sequences 1,
  10, 12, 13, 14, 16, 19, 20, 21, 3, 4, 5, 6, 7, 9, 11, 15, 17, 18, 2,
  22, 8, GL000191.1, GL000192.1, GL000193.1, GL000194.1, GL000195.1,
  GL000196.1, GL000197.1, GL000198.1, GL000199.1, GL000200.1, GL000201.1,
  GL000202.1, GL000203.1, GL000204.1, GL000205.1, GL000206.1, GL000207.1,
  GL000208.1, GL000209.1, GL000210.1, GL000211.1, GL000212.1, GL000213.1,
  GL000214.1, GL000215.1, GL000216.1, GL000217.1, GL000218.1, GL000219.1,
  GL000220.1, GL000221.1, GL000222.1, GL000223.1, GL000224.1, GL000225.1,
  GL000226.1, GL000227.1, GL000228.1, GL000229.1, GL000230.1, GL000231.1,
  GL000232.1, GL000233.1, GL000234.1, GL000235.1, GL000236.1, GL000237.1,
  GL000238.1, GL000239.1, GL000240.1, GL000241.1, GL000242.1, GL000243.1,
  GL000244.1, GL000245.1, GL000246.1, GL000247.1, GL000248.1, GL000249.1,
  MT, X, and Y. Note that ranges located on a sequence whose length is
  unknown (NA) or on a circular sequence are not co [... truncated]
9: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 104 out-of-bound ranges located on sequences 1,
  10, 12, 13, 14, 16, 19, 20, 21, 3, 4, 5, 6, 7, 9, 11, 15, 17, 18, 2,
  22, 8, GL000191.1, GL000192.1, GL000193.1, GL000194.1, GL000195.1,
  GL000196.1, GL000197.1, GL000198.1, GL000199.1, GL000200.1, GL000201.1,
  GL000202.1, GL000203.1, GL000204.1, GL000205.1, GL000206.1, GL000207.1,
  GL000208.1, GL000209.1, GL000210.1, GL000211.1, GL000212.1, GL000213.1,
  GL000214.1, GL000215.1, GL000216.1, GL000217.1, GL000218.1, GL000219.1,
  GL000220.1, GL000221.1, GL000222.1, GL000223.1, GL000224.1, GL000225.1,
  GL000226.1, GL000227.1, GL000228.1, GL000229.1, GL000230.1, GL000231.1,
  GL000232.1, GL000233.1, GL000234.1, GL000235.1, GL000236.1, GL000237.1,
  GL000238.1, GL000239.1, GL000240.1, GL000241.1, GL000242.1, GL000243.1,
  GL000244.1, GL000245.1, GL000246.1, GL000247.1, GL000248.1, GL000249.1,
  MT, X, and Y. Note that ranges located on a sequence whose length is
  unknown (NA) or on a circular sequence are not co [... truncated]
10: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 104 out-of-bound ranges located on sequences 1,
  10, 12, 13, 14, 16, 19, 20, 21, 3, 4, 5, 6, 7, 9, 11, 15, 17, 18, 2,
  22, 8, GL000191.1, GL000192.1, GL000193.1, GL000194.1, GL000195.1,
  GL000196.1, GL000197.1, GL000198.1, GL000199.1, GL000200.1, GL000201.1,
  GL000202.1, GL000203.1, GL000204.1, GL000205.1, GL000206.1, GL000207.1,
  GL000208.1, GL000209.1, GL000210.1, GL000211.1, GL000212.1, GL000213.1,
  GL000214.1, GL000215.1, GL000216.1, GL000217.1, GL000218.1, GL000219.1,
  GL000220.1, GL000221.1, GL000222.1, GL000223.1, GL000224.1, GL000225.1,
  GL000226.1, GL000227.1, GL000228.1, GL000229.1, GL000230.1, GL000231.1,
  GL000232.1, GL000233.1, GL000234.1, GL000235.1, GL000236.1, GL000237.1,
  GL000238.1, GL000239.1, GL000240.1, GL000241.1, GL000242.1, GL000243.1,
  GL000244.1, GL000245.1, GL000246.1, GL000247.1, GL000248.1, GL000249.1,
  MT, X, and Y. Note that ranges located on a sequence whose length is
  unknown (NA) or on a circular sequence are not co [... truncated]
11: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 104 out-of-bound ranges located on sequences 1,
  10, 12, 13, 14, 16, 19, 20, 21, 3, 4, 5, 6, 7, 9, 11, 15, 17, 18, 2,
  22, 8, GL000191.1, GL000192.1, GL000193.1, GL000194.1, GL000195.1,
  GL000196.1, GL000197.1, GL000198.1, GL000199.1, GL000200.1, GL000201.1,
  GL000202.1, GL000203.1, GL000204.1, GL000205.1, GL000206.1, GL000207.1,
  GL000208.1, GL000209.1, GL000210.1, GL000211.1, GL000212.1, GL000213.1,
  GL000214.1, GL000215.1, GL000216.1, GL000217.1, GL000218.1, GL000219.1,
  GL000220.1, GL000221.1, GL000222.1, GL000223.1, GL000224.1, GL000225.1,
  GL000226.1, GL000227.1, GL000228.1, GL000229.1, GL000230.1, GL000231.1,
  GL000232.1, GL000233.1, GL000234.1, GL000235.1, GL000236.1, GL000237.1,
  GL000238.1, GL000239.1, GL000240.1, GL000241.1, GL000242.1, GL000243.1,
  GL000244.1, GL000245.1, GL000246.1, GL000247.1, GL000248.1, GL000249.1,
  MT, X, and Y. Note that ranges located on a sequence whose length is
  unknown (NA) or on a circular sequence are not co [... truncated]
12: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 104 out-of-bound ranges located on sequences 1,
  10, 12, 13, 14, 16, 19, 20, 21, 3, 4, 5, 6, 7, 9, 11, 15, 17, 18, 2,
  22, 8, GL000191.1, GL000192.1, GL000193.1, GL000194.1, GL000195.1,
  GL000196.1, GL000197.1, GL000198.1, GL000199.1, GL000200.1, GL000201.1,
  GL000202.1, GL000203.1, GL000204.1, GL000205.1, GL000206.1, GL000207.1,
  GL000208.1, GL000209.1, GL000210.1, GL000211.1, GL000212.1, GL000213.1,
  GL000214.1, GL000215.1, GL000216.1, GL000217.1, GL000218.1, GL000219.1,
  GL000220.1, GL000221.1, GL000222.1, GL000223.1, GL000224.1, GL000225.1,
  GL000226.1, GL000227.1, GL000228.1, GL000229.1, GL000230.1, GL000231.1,
  GL000232.1, GL000233.1, GL000234.1, GL000235.1, GL000236.1, GL000237.1,
  GL000238.1, GL000239.1, GL000240.1, GL000241.1, GL000242.1, GL000243.1,
  GL000244.1, GL000245.1, GL000246.1, GL000247.1, GL000248.1, GL000249.1,
  MT, X, and Y. Note that ranges located on a sequence whose length is
  unknown (NA) or on a circular sequence are not co [... truncated]
13: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 104 out-of-bound ranges located on sequences 1,
  10, 12, 13, 14, 16, 19, 20, 21, 3, 4, 5, 6, 7, 9, 11, 15, 17, 18, 2,
  22, 8, GL000191.1, GL000192.1, GL000193.1, GL000194.1, GL000195.1,
  GL000196.1, GL000197.1, GL000198.1, GL000199.1, GL000200.1, GL000201.1,
  GL000202.1, GL000203.1, GL000204.1, GL000205.1, GL000206.1, GL000207.1,
  GL000208.1, GL000209.1, GL000210.1, GL000211.1, GL000212.1, GL000213.1,
  GL000214.1, GL000215.1, GL000216.1, GL000217.1, GL000218.1, GL000219.1,
  GL000220.1, GL000221.1, GL000222.1, GL000223.1, GL000224.1, GL000225.1,
  GL000226.1, GL000227.1, GL000228.1, GL000229.1, GL000230.1, GL000231.1,
  GL000232.1, GL000233.1, GL000234.1, GL000235.1, GL000236.1, GL000237.1,
  GL000238.1, GL000239.1, GL000240.1, GL000241.1, GL000242.1, GL000243.1,
  GL000244.1, GL000245.1, GL000246.1, GL000247.1, GL000248.1, GL000249.1,
  MT, X, and Y. Note that ranges located on a sequence whose length is
  unknown (NA) or on a circular sequence are not co [... truncated]
14: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 104 out-of-bound ranges located on sequences 1,
  10, 12, 13, 14, 16, 19, 20, 21, 3, 4, 5, 6, 7, 9, 11, 15, 17, 18, 2,
  22, 8, GL000191.1, GL000192.1, GL000193.1, GL000194.1, GL000195.1,
  GL000196.1, GL000197.1, GL000198.1, GL000199.1, GL000200.1, GL000201.1,
  GL000202.1, GL000203.1, GL000204.1, GL000205.1, GL000206.1, GL000207.1,
  GL000208.1, GL000209.1, GL000210.1, GL000211.1, GL000212.1, GL000213.1,
  GL000214.1, GL000215.1, GL000216.1, GL000217.1, GL000218.1, GL000219.1,
  GL000220.1, GL000221.1, GL000222.1, GL000223.1, GL000224.1, GL000225.1,
  GL000226.1, GL000227.1, GL000228.1, GL000229.1, GL000230.1, GL000231.1,
  GL000232.1, GL000233.1, GL000234.1, GL000235.1, GL000236.1, GL000237.1,
  GL000238.1, GL000239.1, GL000240.1, GL000241.1, GL000242.1, GL000243.1,
  GL000244.1, GL000245.1, GL000246.1, GL000247.1, GL000248.1, GL000249.1,
  MT, X, and Y. Note that ranges located on a sequence whose length is
  unknown (NA) or on a circular sequence are not co [... truncated]
15: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 104 out-of-bound ranges located on sequences 1,
  10, 12, 13, 14, 16, 19, 20, 21, 3, 4, 5, 6, 7, 9, 11, 15, 17, 18, 2,
  22, 8, GL000191.1, GL000192.1, GL000193.1, GL000194.1, GL000195.1,
  GL000196.1, GL000197.1, GL000198.1, GL000199.1, GL000200.1, GL000201.1,
  GL000202.1, GL000203.1, GL000204.1, GL000205.1, GL000206.1, GL000207.1,
  GL000208.1, GL000209.1, GL000210.1, GL000211.1, GL000212.1, GL000213.1,
  GL000214.1, GL000215.1, GL000216.1, GL000217.1, GL000218.1, GL000219.1,
  GL000220.1, GL000221.1, GL000222.1, GL000223.1, GL000224.1, GL000225.1,
  GL000226.1, GL000227.1, GL000228.1, GL000229.1, GL000230.1, GL000231.1,
  GL000232.1, GL000233.1, GL000234.1, GL000235.1, GL000236.1, GL000237.1,
  GL000238.1, GL000239.1, GL000240.1, GL000241.1, GL000242.1, GL000243.1,
  GL000244.1, GL000245.1, GL000246.1, GL000247.1, GL000248.1, GL000249.1,
  MT, X, and Y. Note that ranges located on a sequence whose length is
  unknown (NA) or on a circular sequence are not co [... truncated]
16: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 104 out-of-bound ranges located on sequences 1,
  10, 12, 13, 14, 16, 19, 20, 21, 3, 4, 5, 6, 7, 9, 11, 15, 17, 18, 2,
  22, 8, GL000191.1, GL000192.1, GL000193.1, GL000194.1, GL000195.1,
  GL000196.1, GL000197.1, GL000198.1, GL000199.1, GL000200.1, GL000201.1,
  GL000202.1, GL000203.1, GL000204.1, GL000205.1, GL000206.1, GL000207.1,
  GL000208.1, GL000209.1, GL000210.1, GL000211.1, GL000212.1, GL000213.1,
  GL000214.1, GL000215.1, GL000216.1, GL000217.1, GL000218.1, GL000219.1,
  GL000220.1, GL000221.1, GL000222.1, GL000223.1, GL000224.1, GL000225.1,
  GL000226.1, GL000227.1, GL000228.1, GL000229.1, GL000230.1, GL000231.1,
  GL000232.1, GL000233.1, GL000234.1, GL000235.1, GL000236.1, GL000237.1,
  GL000238.1, GL000239.1, GL000240.1, GL000241.1, GL000242.1, GL000243.1,
  GL000244.1, GL000245.1, GL000246.1, GL000247.1, GL000248.1, GL000249.1,
  MT, X, and Y. Note that ranges located on a sequence whose length is
  unknown (NA) or on a circular sequence are not co [... truncated]
17: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 104 out-of-bound ranges located on sequences 1,
  10, 12, 13, 14, 16, 19, 20, 21, 3, 4, 5, 6, 7, 9, 11, 15, 17, 18, 2,
  22, 8, GL000191.1, GL000192.1, GL000193.1, GL000194.1, GL000195.1,
  GL000196.1, GL000197.1, GL000198.1, GL000199.1, GL000200.1, GL000201.1,
  GL000202.1, GL000203.1, GL000204.1, GL000205.1, GL000206.1, GL000207.1,
  GL000208.1, GL000209.1, GL000210.1, GL000211.1, GL000212.1, GL000213.1,
  GL000214.1, GL000215.1, GL000216.1, GL000217.1, GL000218.1, GL000219.1,
  GL000220.1, GL000221.1, GL000222.1, GL000223.1, GL000224.1, GL000225.1,
  GL000226.1, GL000227.1, GL000228.1, GL000229.1, GL000230.1, GL000231.1,
  GL000232.1, GL000233.1, GL000234.1, GL000235.1, GL000236.1, GL000237.1,
  GL000238.1, GL000239.1, GL000240.1, GL000241.1, GL000242.1, GL000243.1,
  GL000244.1, GL000245.1, GL000246.1, GL000247.1, GL000248.1, GL000249.1,
  MT, X, and Y. Note that ranges located on a sequence whose length is
  unknown (NA) or on a circular sequence are not co [... truncated]
18: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 104 out-of-bound ranges located on sequences 1,
  10, 12, 13, 14, 16, 19, 20, 21, 3, 4, 5, 6, 7, 9, 11, 15, 17, 18, 2,
  22, 8, GL000191.1, GL000192.1, GL000193.1, GL000194.1, GL000195.1,
  GL000196.1, GL000197.1, GL000198.1, GL000199.1, GL000200.1, GL000201.1,
  GL000202.1, GL000203.1, GL000204.1, GL000205.1, GL000206.1, GL000207.1,
  GL000208.1, GL000209.1, GL000210.1, GL000211.1, GL000212.1, GL000213.1,
  GL000214.1, GL000215.1, GL000216.1, GL000217.1, GL000218.1, GL000219.1,
  GL000220.1, GL000221.1, GL000222.1, GL000223.1, GL000224.1, GL000225.1,
  GL000226.1, GL000227.1, GL000228.1, GL000229.1, GL000230.1, GL000231.1,
  GL000232.1, GL000233.1, GL000234.1, GL000235.1, GL000236.1, GL000237.1,
  GL000238.1, GL000239.1, GL000240.1, GL000241.1, GL000242.1, GL000243.1,
  GL000244.1, GL000245.1, GL000246.1, GL000247.1, GL000248.1, GL000249.1,
  MT, X, and Y. Note that ranges located on a sequence whose length is
  unknown (NA) or on a circular sequence are not co [... truncated]
19: In score.hypotheses(targ, sets = sets, covariates = covs,  ... :
  negative binomial failed to converge, automatically running poisson

[pushpa-itagi]

Hi,

I have the same error coming up
Error in aggregate.formula(formula = subject.id ~ grl.id, data = m, FUN = function(x) numwin - : argument 'x' is missing -- it has been renamed from 'formula' Calls: events ... .local -> grl.in -> -> aggregate.formula
Please let us know if there is a fix. Could it be some dependency R library issue?I am using R/4.2 and the github suggests it should be any version greater than 3.6, so it should ideally work.
Thanks!
Pushpa

[manojbhagwat123]

Hi @pushpa-itagi

I ended up resolving the issue with generating the events() metadata; however, the aforementioned hidden warnings() that I got remained. The exact same errors were present when I ran the gGnome tutorial code though, and the output even with these hidden warnings matched the counts shown in the gGnome tutorial, so take that as you will.

The source of the argument 'x' is missing within the aggregate.formula error is an update that started in R version 4.2.0. You can look at this within the few bullet points in this R Documentation: R Changes In R 4.2.0.

I fixed this by using a Conda environment to run R version 4.1.3. Using this version, I was able to generate the events() metadata without getting the argument 'x' is missing within the aggregate.formula error. If you want some details on how I made this Conda environment:

conda create -n r_env_4.1.3 -c conda-forge r-base=4.1.3
conda init
#Then, restart your shell (log out and log back in, or run source ~/.bashrc)
conda activate r_env_4.1.3
conda install -c conda-forge r-devtools r-testthat
conda install -c conda-forge gxx_linux-64 gcc_linux-64 gfortran_linux-64 #I think this would be different if you're on Mac, and I'm also not sure how necessary this line is
#After this I just ran “R” in the terminal, which would bring up R 4.1.3 interactively. Here, after loading the devtools and testthat packages, I struggled to get the devtools::install_github('mskilab/gGnome') to work. I did not write down the exact steps as I fixed this, but here is a rough idea of how I worked around it after struggling for a while. Hopefully this is the bare minimum for correct installation, if not there may be other dependencies you would also need to install either manually or somehow through conda install prior to downloading bamUtils, gUtils, or gGnome:
#Within r_env_4.1.3 (but not in interactive R)
conda config --add channels defaults 
conda config --add channels bioconda 
conda config --add channels conda-forge
conda update -n base -c defaults conda
conda install bioconductor-genomicranges
conda install bioconductor-rtracklayer
conda install bioconductor-biostrings
conda install bioconductor-genomicalignments
conda install bioconductor-gtrack
conda install -c conda-forge r-igraph
R
library(devtools)
library(testthat)
Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS = TRUE)
devtools::install_github('mskilab/bamUtils')
devtools::install_github('mskilab/gUtils')
#Then, I manually installed gGnome from the GitHub using the tar.gz instead of using devtools

The GitHub (or gGnome tutorial) should definitely update, at the very least, the fact that events() loses functionality from R version 4.2.0 onwards.

I hope this helps.

Sincerely,
Manoj

[pushpa-itagi]

@manojbhagwat123 Thanks you so much for the quick details given. Ill try going to a lower version of R < 4.2.0 and then use gGnome.

[mingwhy]

Thank you for this information!

The source of the argument 'x' is missing within the aggregate.formula error is an update that started in R version 4.2.0. You can look at this within the few bullet points in this R Documentation: R Changes In R 4.2.0.

And also what I saw in another issue in JaBbA repo, which kindly showed the modification of code in gTrack.R

Please see commit 4aa01d0 of gTrack, which addresses this error.

to solve this aggregate function issue.

I tried to create a conda environment to run R version 4.1.3. However, it might be that my laptop is a M3 chip mac (R_PLATFORM aarch64-apple-darwin20), it failed to install those required R packages such as r-devtools and r-testthat. So below is what I did:

In Rstudio with R version 4.4.1

library(gGnome)
hcc1954 = gG(jabba = system.file("extdata", "hcc1954", "jabba.rds", package = "gGnome"))
hcc1954 = events(hcc1954, verbose = T)

error message popped out:

Finished simple
Finished amp (tyfonas, dm, cpxdm, bfb)
Finished chromothripsis
Loading required package: MASS
Error in aggregate.formula(formula = subject.id ~ grl.id, data = m, FUN = function(x) numwin -  : 
  argument 'x' is  missing -- it has been renamed from 'formula'
In addition: There were 18 warnings (use warnings() to see them)

So events function ran into some error after finishing detecting chromothripsis step.
I checked source code of events function in eventCallers.R, and located the code line after Finished chromothripsis. It's gg = gg %>% del(mark = TRUE).

Digging into function del, and excute line by line, I saw the error came from simple.dels = all.dels[!(all.dels %^% (sig %Q% (count>1))) & !(all.dels %^% (other$shadow+tile.width))]

I tested (sig %Q% (count>1), it went on well. Then (all.dels %^% (sig %Q% (count>1))), error happened.

%^% was defined in gGnome.R. Similarly, debug line by line, the error actually came from grl.in function from gUtils pacakge.

Checking source code for gUtils.R, I saw this line:

tmp = stats::aggregate(formula = subject.id ~ grl.id, data = m, FUN = function(x) numwin-length(setdiff(1:numwin, x)))

which is exactly the error message.

So, here is my solution:
I downloaded gUtils.R to my laptop as file re_gUtils.R and changed the above line into:

tmp = stats::aggregate(x = subject.id ~ grl.id, data = m, FUN = function(x) numwin-length(setdiff(1:numwin, x)))

Then I extracted those code chunks defining %^% in gGnome.R and saved it to re_setMethod.R file.

Then In Rstudio, I ran:

library(gGnome);
hcc1954 = gG(jabba = system.file("extdata", "hcc1954", "jabba.rds", package = "gGnome"))
hcc1954 = events(hcc1954, verbose = TRUE) #error happened

source('~/Downloads/re_gUtils.R') 
source('~/Downloads/re_setMethod.R')
grl.in #make sure that this function is updated

hcc1954 = events(hcc1954, verbose = TRUE) #run smoothly

#following tutorial in http://www.mskilab.com.s3-website-us-east-1.amazonaws.com/gGnome/tutorial.html#Classifying_SV_events 
hcc1954$meta$event[, table(type)] 
plot(hcc1954$gt, hcc1954[bfb>0]$footprint + 1e6); title("BFB in HCC1954")

re_load_funcs.zip

[jrafailov]

Hi all, thanks for using our tool and bringing our attention to this issue. You're exactly correct the errors you are facing are attributable to the aggregate function that has changed within R4.2+. we have adjusted gGnome and gUtils accordingly to reconcile the new function call with nameless, positional parameters

please see:
#158
mskilab-org/gUtils#47

closing ticket as well

[manojbhagwat123]

Hi @jrafailov,

I updated gGnome to the latest version just now (af4ba04 commit), as well as gUtils (fc24db6 commit), I am now getting a "Error: object 'min.cushion' not found" error when trying to run events(). This results in the events metadata not even being generated. This occurs not only with my jabba.rds files, but also when trying to use the gGnome tutorial code. Do you know why this is the case?

Sincerely,
Manoj