homer分析pca之多样本比较

homer分析pca之多样本比较https://wiki.bits.vib.be/index.php/Homer
》》》》》首先呀安装limma包
#######
!!! Warnining - something likely failed during R execution.
!!! R script that was used:
####### basic script for running limma for PC1/TADs (generated by HOMER) ########
#### input is matrix data - first column is TAD id, others are TAD inclusion scores
#### Exp1 Exp2
#### chr1:300000-400000 2.45 2.01
library(limma)
#Read Data in
countData <- read.delim(“0.560185876981453.edgeR.in.data.txt”,row.names=1)
colData <- read.delim(“0.560185876981453.edgeR.groups.data.txt”)

design <-model.matrix(~Treatment, data=colData)
fit <- lmFit(countData, design)
fit2 <- eBayes(fit)
res <- topTable(fit2,n=Inf)
tidyResult <- data.frame(TAD=rownames(res), res)
write.table(tidyResult,file="0.560185876981453.edgeR.out.data.txt",sep="\t",row.names=FALSE)

!!! R execution details:
Error in library(limma) : there is no package called ‘limma’
Execution halted

》》》》》》》

##step3
#If you have PC1 bedGraphs from replicate experiments across two conditions, you can identify significantly changing compartments using the following:
annotatePeaks.pl /data/zhangyong/yyp/yypold/hic/hicdata/validpairs/valid/WT_DM_BL-HiC_Rep1.allValidPairs-HiC/WT_DM_BL-HiC_Rep1.allValidPairs-HiC.25x50kb.PC1.txt mm10 -noblanks -bedGraph /data/zhangyong/yyp/yypold/hic/hicdata/pca/WT_DM_BL-HiC_Rep1.allValidPairs-HiC.25x50kb.PC1.bedGraph /data/zhangyong/yyp/yypold/hic/hicdata/pca/WT_DM_BL-HiC_Rep2.allValidPairs-HiC.25x50kb.PC1.bedGraph /data/zhangyong/yyp/yypold/hic/hicdata/pca/WT_GM_BL-HiC_Rep1.allValidPairs-HiC.25x50kb.PC1.bedGraph /data/zhangyong/yyp/yypold/hic/hicdata/pca/WT_GM_BL-HiC_Rep2.allValidPairs-HiC.25x50kb.PC1.bedGraph > outputstep3.txt
getDiffExpression.pl outputstep3.txt DM DM GM GM -pc1 -export outputPrefix > output2Diff.txt

Peak file = /data/zhangyong/yyp/yypold/hic/hicdata/validpairs/valid/WT_DM_BL-HiC_Rep1.allValidPairs-HiC/WT_DM_BL-HiC_Rep1.allValidPairs-HiC.25x50kb.PC1.txt
Genome = mm10
Organism = mouse
Will remove rows with data values of '' or 'NA'
bedGraph Files:
	/data/zhangyong/yyp/yypold/hic/hicdata/pca/WT_DM_BL-HiC_Rep1.allValidPairs-HiC.25x50kb.PC1.bedGraph
	/data/zhangyong/yyp/yypold/hic/hicdata/pca/WT_DM_BL-HiC_Rep2.allValidPairs-HiC.25x50kb.PC1.bedGraph
	/data/zhangyong/yyp/yypold/hic/hicdata/pca/WT_GM_BL-HiC_Rep1.allValidPairs-HiC.25x50kb.PC1.bedGraph
	/data/zhangyong/yyp/yypold/hic/hicdata/pca/WT_GM_BL-HiC_Rep2.allValidPairs-HiC.25x50kb.PC1.bedGraph
Peak/BED file conversion summary:
	BED/Header formatted lines: 0
	peakfile formatted lines: 103857
	Duplicated Peak IDs: 0

Peak File Statistics:
	Total Peaks: 103857
	Redundant Peak IDs: 0
	Peaks lacking information: 0 (need at least 5 columns per peak)
	Peaks with misformatted coordinates: 0 (should be integer)
	Peaks with misformatted strand: 0 (should be either +/- or 0/1)

Peak file looks good!

Reading Positions...
-----------------------
Finding Closest TSS...
Annotating:.............................
	Annotation	Number of peaks	Total size (bp)	Log2 Ratio (obs/exp)	LogP enrichment (+values depleted)
	3UTR	847.0	20769155	0.097	-3.631
	miRNA	1.0	31126	-0.247	0.404
	ncRNA	130.0	3444819	-0.015	0.741
	TTS	1041.0	27332353	-0.001	0.702
	pseudo	20.0	554446	-0.080	0.779
	Exon	1394.0	34653721	0.077	-3.760
	Intron	37785.0	950229103	0.061	-54.352
	Intergenic	61361.0	1653660826	-0.039	60.235
	Promoter	1143.0	30220057	-0.011	0.914
	5UTR	101.0	2376100	0.157	-1.904
	snoRNA	0.0	19	-0.001	0.001
	rRNA	0.0	5631	-0.281	0.215
NOTE: If this part takes more than 2 minutes, there is a good chance
	your machine ran out of memory: consider hitting ctrl+C and rerunning
	the command with "-noann"
To capture annotation stats in a file, use "-annStats <filename>" next time
Annotating:.........................................
	Annotation	Number of peaks	Total size (bp)	Log2 Ratio (obs/exp)	LogP enrichment (+values depleted)
	3UTR	847.0	20769155	0.098	-3.667
	Other	288.0	7952166	-0.073	1.596
	RC?	1.0	10979	1.257	-1.073
	RNA	5.0	113962	0.203	-0.826
	miRNA	1.0	31126	-0.246	0.404
	ncRNA	130.0	3444819	-0.014	0.735
	TTS	1041.0	27332353	-0.001	0.688
	LINE	21179.0	544526405	0.030	-7.739
	LINE?	1.0	8168	1.684	-1.319
	srpRNA	2.0	43307	0.277	-0.711
	SINE	7891.0	196555829	0.075	-13.912
	RC	4.0	65629	0.678	-1.416
	tRNA	13.0	266727	0.355	-1.495
	DNA?	8.0	142070	0.563	-1.715
	pseudo	20.0	554446	-0.079	0.776
	DNA	1137.0	28683535	0.057	-2.372
	Exon	1394.0	34653721	0.078	-3.807
	Intron	23990.0	602909260	0.062	-31.534
	Intergenic	29211.0	823289671	-0.103	111.499
	Promoter	1143.0	30220057	-0.011	0.896
	5UTR	101.0	2376100	0.158	-1.912
	snoRNA	0.0	19	-0.001	0.001
	LTR?	4.0	192563	-0.875	1.935
	scRNA	23.0	602525	0.003	-0.646
	CpG-Island	152.0	3122603	0.353	-6.205
	Low_complexity	754.0	19402023	0.028	-1.209
	LTR	12054.0	313371409	0.014	-1.994
	Simple_repeat	2232.0	57559904	0.025	-1.588
	snRNA	10.0	237324	0.145	-0.872
	Unknown	67.0	2405524	-0.452	5.461
	SINE?	3.0	29758	1.404	-2.240
	Satellite	149.0	4592921	-0.232	3.705
	rRNA	2.0	166488	-1.665	3.031
Counting Tags in Peaks from each directory...
Organism: mouse
Loading Gene Informaiton...
Outputing Annotation File...
Removed 0 with missing data (out of 103857)
Done annotating peaks file

Treating input as file generated by annotatePeaks.pl (-peaks)
Will report raw counts in output table (no normalization)
Using limma to calculate differential expression/enrichment...
Output Stats DM vs. GM:
	Total Genes: 103250
	Total Up-regulated in GM vs. DM: 313 (0.303%) [log2fold>1, FDR<0.05]
	Total Dn-regulated in GM vs. DM: 301 (0.292%) [log2fold<-1, FDR<0.05]

	Total continuous domains: 26 (Up) and 24 (Down)