Hi,
I wound like to get 2,913 consensus peaks that in Early stage, but not in Late stage samples (fig1). They are overlapping between T8E_HMC & T9E_HMC samples, but not in T8L_HMC and T9L_HMC samples (fig1). I have tried the dba.peakset command, but doesn't work. Could you show me how to do it correctly? The best way is to get a .bed file for the downstream analysis. Below are commands I used to get this Venn diagram for your reference. Thank you so much.
Best,
Gary
> t8t9=dba(sampleSheet = "t8t9.csv",peakFormat = "bed")
T8E_HMC MSC Early T8 1 MACS
T9E_HMC MSC Early T9 2 MACS
T8L_HMC MSC Late T8 1 MACS
T9L_HMC MSC Late T9 2 MACS
> t8t9
4 Samples, 15919 sites in matrix (39174 total):
ID Tissue Factor Condition Replicate Caller Intervals
1 T8E_HMC MSC Early T8 1 MACS 21905
2 T9E_HMC MSC Early T9 2 MACS 23327
3 T8L_HMC MSC Late T8 1 MACS 12377
4 T9L_HMC MSC Late T9 2 MACS 12902
> names(t8t9$masks)
[1] "MSC" "Early" "Late" "T8" "T9" "" "MACS" "Replicate.1" "Replicate.2" "All"
[11] "None"
> dba.plotVenn(t8t9,t8t9$masks$MSC)
fig1
Hi Rory,
Thank you so much. I have tried what you suggested, but I don't know how to save the result as a txt file. I know it's not a DiffBind question, but could you help me again? Many thanks. Below are command lines I used for your reference.
Best,
Gary
> t8t9=dba(sampleSheet = "t8t9.csv",peakFormat = "bed")
T8E_HMC MSC Early T8 1 MACS
T9E_HMC MSC Early T9 2 MACS
T8L_HMC MSC Late T8 1 MACS
T9L_HMC MSC Late T9 2 MACS
> t8t9
4 Samples, 15919 sites in matrix (39174 total):
ID Tissue Factor Condition Replicate Caller Intervals
1 T8E_HMC MSC Early T8 1 MACS 21905
2 T9E_HMC MSC Early T9 2 MACS 23327
3 T8L_HMC MSC Late T8 1 MACS 12377
4 T9L_HMC MSC Late T9 2 MACS 12902
> names(t8t9$masks)
[1] "MSC" "Early" "Late" "T8" "T9" ""
[7] "MACS" "Replicate.1" "Replicate.2" "All" "None"
> dba.plotVenn(t8t9, t8t9$masks$MSC)
> t8t9.overlaps <-dba.overlap(t8t9,t8t9$masks$MSC)
> names(t8t9.overlaps)
[1] "onlyA" "onlyB" "onlyC" "onlyD" "AandB" "AandC" "AandD" "BandC" "BandD" "CandD" "notA"
[12] "notB" "notC" "notD" "inAll"
> t8t9.overlaps$AandB
GRanges object with 2913 ranges and 2 metadata columns:
seqnames ranges strand | scoreA scoreB
<Rle> <IRanges> <Rle> | <numeric> <numeric>
24 chr1 [ 564352, 570445] * | 0.046839174582378 0.0234009360374415
55 chr1 [ 900161, 901002] * | 0.0167048804454635 0.0227769110764431
71 chr1 [1009781, 1010682] * | 0.0347199475925319 0.0277691107644306
77 chr1 [1047306, 1048373] * | 0.0252210940058958 0.0162246489859594
94 chr1 [1218174, 1218917] * | 0.0212905339010809 0.0287051482059282
... ... ... ... ... ... ...
39020 chrY [ 2427812, 2428479] * | 0.0370127743203406 0.0271450858034321
39091 chrY [10018797, 10020074] * | 0.0216180805764821 0.0168486739469579
39125 chrY [13671130, 13672096] * | 0.0458565345561743 0.0215288611544462
39127 chrY [13682255, 13683846] * | 0.0255486406812971 0.0290171606864275
39137 chrY [13816319, 13823737] * | 0.0674746151326564 0.0464898595943838
-------
seqinfo: 33 sequences from an unspecified genome; no seqlengths
> write.table(t8t9.overlaps$AandB,"./t8t9.overlapsAandB.txt")
Error in as.vector(x) : no method for coercing this S4 class to a vector
> write.table(t8t9.overlaps$AandB,file="t8t9overlapsAandB.txt")
Error in as.vector(x) : no method for coercing this S4 class to a vector
Look here
A: diffbind: exporting unique peak sets
Thanks a lot.
Thanks a lot.