hello，I don't know how to deal with it，can you help me figure it out. thanks about chippeakanno HOT 8 OPEN

try to remove the duplicated ranges from your inputs. You may want to try

tmp_rd <- lapply(tmp, reduce)
ol <- findOverlapsOfPeaks(tmp_rd)

from chippeakanno.

try to remove the duplicated ranges from your inputs. You may want to try

tmp_rd <- lapply(tmp, reduce)
ol <- findOverlapsOfPeaks(tmp_rd)

sorry，it has another error

tmp_rd <- lapply(tmp, reduce)
ol <- findOverlapsOfPeaks(tmp_rd)

Error in findOverlapsOfPeaks(tmp_rd) :
The length of input peaks list should no more than 5

from chippeakanno.

try

tmp_rd <- lapply(tmp, reduce)
ol <- do.call(findOverlapsOfPeaks, tmp_rd)

or

tmp_rd <- lapply(tmp, reduce)
ol <- findOverlapsOfPeaks(tmp_rd[[1]], tmp_rd[[2]], tmp_rd[[3]])

from chippeakanno.

try

tmp_rd <- lapply(tmp, reduce)
ol <- do.call(findOverlapsOfPeaks, tmp_rd)

or

tmp_rd <- lapply(tmp, reduce)
ol <- findOverlapsOfPeaks(tmp_rd[[1]], tmp_rd[[2]], tmp_rd[[3]])

thanks，but sorry again ，it still has some error，i think that my data maybe have something wrong with it.

tmp_rd <- lapply(tmp, reduce)

ol <- do.call(findOverlapsOfPeaks, tmp_rd)
Error in names(PeaksList) <- names :
'names' attribute [242484] must be the same length as the vector [6]

tmp_rd <- lapply(tmp, reduce)
ol <- findOverlapsOfPeaks(tmp_rd[[1]], tmp_rd[[2]], tmp_rd[[3]])
duplicated or NA names found.
Rename all the names by numbers.
duplicated or NA names found.
Rename all the names by numbers.
duplicated or NA names found.
Rename all the names by numbers.
Warning messages:
1: In .merge_two_Seqinfo_objects(x, y) :
Each of the 2 combined objects has sequence levels not in the other:

• in 'x': chrUn_NW_020190156v1, chrUn_NW_020190179v1, chrUn_NW_020190198v1, chrUn_NW_020190245v1, chrUn_NW_020190261v1, chrUn_NW_020190317v1, chrUn_NW_020190350v1, chrUn_NW_020190386v1, chrUn_NW_020190407v1, chrUn_NW_020190443v1, chrUn_NW_020190469v1, chrUn_NW_020190492v1, chrUn_NW_020190512v1, chrUn_NW_020190522v1, chrUn_NW_020190573v1, chrUn_NW_020190623v1, chrUn_NW_020190632v1, chrUn_NW_020190639v1, chrUn_NW_020190641v1, chrUn_NW_020190656v1, chrUn_NW_020190672v1, chrUn_NW_020190682v1, chrUn_NW_020190714v1, chrUn_NW_020190754v1, chrUn_NW_020190767v1, chrUn_NW_020190771v1, chrUn_NW_020190784v1, chrUn_NW_020190801v1, chrUn_NW_020190839v1, chrUn_NW_020190859v1, chrUn_NW_020190906v1, chrUn_NW_020190984v1, chrUn_NW_020190999v1, chrUn_NW_020191007v1, chrUn_NW_020191022v1, chrUn_NW_020191162v1, chrUn_NW_020191168v1, chrUn_NW_020191203v1, chrUn_NW_020191224v1, chrUn_NW_020191226v1, chrUn_NW_020191251v1, chrUn_NW_02019131 [... truncated]
  2: In .merge_two_Seqinfo_objects(x, y) :
  Each of the 2 combined objects has sequence levels not in the other:
• in 'x': chrUn_NW_020190132v1, chrUn_NW_020190142v1, chrUn_NW_020190198v1, chrUn_NW_020190245v1, chrUn_NW_020190289v1, chrUn_NW_020190317v1, chrUn_NW_020190386v1, chrUn_NW_020190407v1, chrUn_NW_020190492v1, chrUn_NW_020190511v1, chrUn_NW_020190512v1, chrUn_NW_020190530v1, chrUn_NW_020190537v1, chrUn_NW_020190573v1, chrUn_NW_020190621v1, chrUn_NW_020190623v1, chrUn_NW_020190636v1, chrUn_NW_020190639v1, chrUn_NW_020190656v1, chrUn_NW_020190672v1, chrUn_NW_020190754v1, chrUn_NW_020190756v1, chrUn_NW_020190767v1, chrUn_NW_020190784v1, chrUn_NW_020190984v1, chrUn_NW_020190999v1, chrUn_NW_020191022v1, chrUn_NW_020191045v1, chrUn_NW_020191078v1, chrUn_NW_020191082v1, chrUn_NW_020191093v1, chrUn_NW_020191162v1, chrUn_NW_020191203v1, chrUn_NW_020191211v1, chrUn_NW_020191220v1, chrUn_NW_020191224v1, chrUn_NW_020191232v1, chrUn_NW_020191240v1, chrUn_NW_020191251v1, chrUn_NW_020191273v1, chrUn_NW_020191311v1, chrUn_NW_02019131 [... truncated]
  3: In .merge_two_Seqinfo_objects(x, y) :
  Each of the 2 combined objects has sequence levels not in the other:
• in 'x': chrUn_NW_020190132v1, chrUn_NW_020190138v1, chrUn_NW_020190142v1, chrUn_NW_020190148v1, chrUn_NW_020190201v1, chrUn_NW_020190289v1, chrUn_NW_020190318v1, chrUn_NW_020190319v1, chrUn_NW_020190324v1, chrUn_NW_020190326v1, chrUn_NW_020190328v1, chrUn_NW_020190372v1, chrUn_NW_020190393v1, chrUn_NW_020190411v1, chrUn_NW_020190449v1, chrUn_NW_020190464v1, chrUn_NW_020190496v1, chrUn_NW_020190511v1, chrUn_NW_020190530v1, chrUn_NW_020190537v1, chrUn_NW_020190539v1, chrUn_NW_020190542v1, chrUn_NW_020190555v1, chrUn_NW_020190557v1, chrUn_NW_020190621v1, chrUn_NW_020190636v1, chrUn_NW_020190658v1, chrUn_NW_020190679v1, chrUn_NW_020190692v1, chrUn_NW_020190746v1, chrUn_NW_020190756v1, chrUn_NW_020190810v1, chrUn_NW_020190811v1, chrUn_NW_020190821v1, chrUn_NW_020190858v1, chrUn_NW_020190942v1, chrUn_NW_020190945v1, chrUn_NW_020190983v1, chrUn_NW_020191025v1, chrUn_NW_020191036v1, chrUn_NW_020191045v1, chrUn_NW_02019107 [... truncated]

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I think the second try works. Try to plot the data via

makeVennDiagram(ol)

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thanks!!! it works!!!but there has some warning messages,i think it doesn't matter

Warning messages:
1: In phyper(a.and.b - 1, b, totalTest - b, a, lower.tail = FALSE, :
产生了NaNs
2: In phyper(a.and.b - 1, b, totalTest - b, a, lower.tail = FALSE, :
产生了NaNs

from chippeakanno.

The warning from findOverlapsOfPeaks indicates that the peaklist contain incompatible chromosome names. Please double check if it affect the results. You can trim those peaks with patched chromosome names.
The warning message from makeVennDiagram means it can not create p value for overlapping test via phyper.

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Thank you, your help is much appreciated！！！

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