I'm a new with DiffBind for differential binding analysis of ChIP-Seq peak data.I want to write command line for my work.But always print error.I really don't understant with dba.contrast and dba.mask.
I have 4 samples with chip-experiment,they are A_K2、B_T1、B_T3 and B_H3.And I have got 4 file peaks for every sample with Input sample(no-chip).
Now,I want get the differential binding of 3 combinations,A_K2vsB_T1、A_K2vsB_T3 and A_K2vsB_H3.My DBA sampleSheet is as follow:
SampleID Tissue Factor Condition Treatment Replicate
1 A_K2 A_K2vsB_T1 ER Resistant Full 1
2 B_T1 A_K2vsB_T1 ER Responsive Full 1
3 B_T3 A_K2vsB_T3 ER Responsive Full 1
4 B_H3 A_K2vsB_H3 ER Responsive Full 1
bamReads ControlID bamControl
1 Sample_150079A_K2.bam B_Input Sample_150079B_Input.bam
2 Sample_150079B_T1.bam B_Input Sample_150079B_Input.bam
3 Sample_150079B_T3.bam B_Input Sample_150079B_Input.bam
4 Sample_150079B_H3.bam B_Input Sample_150079B_Input.bam
Peaks PeakCaller PeakFormat
1 run_macs14_narrow1_peaks.bed bed bed
2 run_macs14_narrow2_peaks.bed bed bed
3 run_macs14_narrow3_peaks.bed bed bed
4 run_macs14_narrow4_peaks.bed bed bed
>diff <- dba(sampleSheet="sample.csv")
>diff_count <- dba.count(diff,minOverlap=1)
I really need your help about dba.contrast and dba.analyze.
Thank you so much.