Comments (8)
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]
from chippeakanno.
I think the second try works. Try to plot the data via
makeVennDiagram(ol)
from chippeakanno.
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.
from chippeakanno.
Thank you, your help is much appreciated!!!
from chippeakanno.
Related Issues (20)
- genomicElementDistribution not found HOT 5
- Error with `bindingType` in `annotatePeakInBatch` HOT 2
- toGRanges() no longer working in response to UCSC update HOT 3
- Questions on the how genomicElementDistribution works HOT 1
- error in enrichmentPlot() when providing a partially empty GO object HOT 1
- toGRanges() can't read in file name HOT 1
- Differences between bedtools overlap / findOverlaps and findOverlapsOfPeaks HOT 10
- disjointExons removed in Bioconductor 3.17 HOT 1
- How to understand otherExon HOT 7
- `findOverlapsOfPeaks(gr1, gr2)` Error in FUN(X[[i]], ...) : Inputs contains duplicated ranges. please recheck your inputs. HOT 6
- How to set the circle size same proportion of the number of peaks when there are more than 2 sets using `makeVennDiagram`? HOT 5
- oligoSummary not populating the motif matrix output field HOT 2
- makeVennDiagram fails with error 'Unexpected parameter length for "col"' HOT 4
- cvglists rtracklayer import error: Error in stop_if_wrong_length(what, ans_len) 'ranges' must have the length of the object to construct HOT 4
- makeVennDiagram produces undesired console output HOT 6
- Regarding oligoSummary() HOT 1
- opened in error
- anno gene in heatmap HOT 4
- Number of Overlap Peaks HOT 1
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