Hello, I am running Diffbind for Cut&Run data. It is from rare types of tumors that unfortunately was not possible to create replicates. However I have data from different tumors subgroup (1, 3 and 4) as showed in the sample sheet below.
diff SampleID Factor Tissue Condition bamReads Peaks 1 Chord86b H3K4me3 tumor grupo1 210610_I105_V350004499_L2_Chord-86b-H3K4me3.bam 210610_I105_V350004499_L2_Chord-86b-H3K4me3_seacr.peaks.stringent.sort.bed 2 Chord30b H3K4me3 tumor grupo1 210610_I105_V350004499_L1_Chord-30b-H3K4me3.bam 210610_I105_V350004499_L1_Chord-30b-H3K4me3_seacr.peaks.stringent.sort.bed 3 Chord35 H3K4me3 tumor grupo3 210610_I105_V350004499_L2_Chord-35-H3K4me3-1.bam 210610_I105_V350004499_L2_Chord-35-H3K4me3-1_seacr.peaks.stringent.sort.bed 4 Chord18b H3K4me3 tumor grupo3 210610_I105_V350004499_L2_Chord-18b-H3K4me3.bam 210610_I105_V350004499_L2_Chord-18b-H3K4me3_seacr.peaks.stringent.sort.bed 5 Chord21 H3K4me3 tumor grupo4 210610_I105_V350004499_L2_Chord-21-H3K4me3.bam 210610_I105_V350004499_L2_Chord-21-H3K4me3_seacr.peaks.stringent.sort.bed 6 Chord10a H3K4me3 tumor grupo4 210301_I23_V300101150_L4_Chord10a-H3K4me3.bam 210301_I23_V300101150_L4_Chord10a-H3K4me3_seacr.peaks.stringent.sort.bed Peakcaller 1 seacr 2 seacr 3 seacr 4 seacr 5 seacr 6 seacr
I would like to identify peaks that are different and similar between samples of the same group and also identify differences between groups. However I don't know how to establish contrast for my analysis, I feel like I shouldn't use 'minMembers = 2', but reading the 'dba.contrast()' function I think I should specify what I want to compare. If someone could give me a hint in how to do that would be great, I am kind of new in bioinfo.
sessionInfo( ) R version 4.1.0 (2021-05-18) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19042) ```