Hi ,
I run a full script of MEDIPS and got output like this --
chr | start | stop | CF | SampleC_result.bam.counts | SampleD_result.bam.counts | SampleC_result.bam.rpkm | SampleD_result.bam.rpkm | SampleC_result.bam.rms | SampleD_result.bam.rms | MSets1.counts.mean | MSets1.rpkm.mean | MSets1.rms.mean | MSets2.counts.mean | MSets2.rpkm.mean | MSets2.rms.mean | edgeR.logFC | edgeR.logCPM | edgeR.p.value | edgeR.adj.p.value | 1_id | 2_id | |
869 | chr1 | 86801 | 86900 | 3 | 21 | 66 | 28.91 | 100.77 | 0.66 | 0.83 | 21 | 28.91 | 0.66 | 66 | 100.77 | 0.83 | -1.7920893719 | 2.7474174303 | 8.33654332196427E-08 | 0.0172985775 | NA | NA |
2000066 | chr1 | 200006501 | 200006600 | 4 | 37 | 0 | 50.94 | 0 | 0.73 | 0 | 37 | 50.94 | 0.73 | 0 | 0 | 0 | 8.1432140516 | 1.5378794034 | 3.00335172395078E-11 | 0.000006232 | NA | NA |
2000067 | chr1 | 200006601 | 200006700 | 6 | 48 | 0 | 66.08 | 0 | 0.73 | 0 | 48 | 66.08 | 0.73 | 0 | 0 | 0 | 8.5175532823 | 1.8761919171 | 2.99277412121177E-14 | 6.21009608473806E-09 | NA | NA |
2000068 | chr1 | 200006701 | 200006800 | 9 | 42 | 1 | 57.82 | 1.53 | 0.67 | 0.12 | 42 | 57.82 | 0.67 | 1 | 1.53 | 0.12 | 5.0886311128 | 1.7339671371 | 3.96394127476866E-11 | 8.22529706338322E-06 | NA | NA |
2000069 | chr1 | 200006801 | 200006900 | 5 | 27 | 1 | 37.17 | 1.53 | 0.66 | 0.18 | 27 | 37.17 | 0.66 | 1 | 1.53 | 0.18 | 4.4536975675 | 1.1871136508 | 4.23547920710291E-07 | 0.0878874642 | NA | NA |
2097234 | chr1 | 209723301 | 209723400 | 1 | 0 | 28 | 0 | 42.75 | 0 | 0.77 | 0 | 0 | 0 | 28 | 42.75 | 0.77 | -7.8885206568 | 1.242042544 | 3.80157670010712E-09 | 0.0007888386 | NA | NA |
2105738 | chr1 | 210573701 | 210573800 | 1 | 27 | 1 | 37.17 | 1.53 | 0.75 | 0.28 | 27 | 37.17 | 0.75 | 1 | 1.53 | 0.28 | 4.4536975675 | 1.1871136508 | 4.23547920710291E-07 | 0.0878874642 | NA | NA |
2163247 | chr1 | 216324601 | 216324700 | 2 | 0 | 22 | 0 | 33.59 | 0 | 0.7 | 0 | 0 | 0 | 22 | 33.59 | 0.7 | -7.5422568331 | 0.9382190482 | 2.41450299325845E-07 | 0.0501016615 | ENSSSCG00000005207 | NA |
2271159 | chr1 | 227115801 | 227115900 | 1 | 0 | 23 | 0 | 35.12 | 0 | 0.74 | 0 | 0 | 0 | 23 | 35.12 | 0.74 | -7.6060506188 | 0.9934313723 | 1.20863824109425E-07 | 0.0250796061 | NA | NA |
3129473 | chr1 | 312947201 | 312947300 | 1 | 38 | 4 | 52.31 | 6.11 | 0.8 | 0.48 | 38 | 52.31 | 0.8 | 4 | 6.11 | 0.48 | 3.0643134186 | 1.7084900082 | 4.54579647734759E-07 | 0.0943266406 | NA | NA |
3130975 | chr1 | 313097401 | 313097500 | 1 | 68 | 15 | 93.61 | 22.9 | 0.89 | 0.68 | 68 | 93.61 | 0.89 | 15 | 22.9 | 0.68 | 2.0255720997 | 2.6267801872 | 3.8638156315668E-08 | 0.0080175333 | NA | NA |
3309724 | chr2 | 15650901 | 15651000 | 1 | 27 | 1 | 37.17 | 1.53 | 0.75 | 0.28 | 27 | 37.17 | 0.75 | 1 | 1.53 | 0.28 | 4.4536975675 | 1.1871136508 | 4.23547920710291E-07 | 0.0878874642 | ENSSSCG00000013248 | NA |
3309725 | chr2 | 15651001 | 15651100 | 2 | 28 | 1 | 38.55 | 1.53 | 0.73 | 0.25 | 28 | 38.55 | 0.73 | 1 | 1.53 | 0.25 | 4.5059155442 | 1.230895305 | 2.19611172180891E-07 | 0.0455699771 | ENSSSCG00000013248 | NA |
3309726 | chr2 | 15651101 | 15651200 | 1 | 27 | 0 | 37.17 | 0 | 0.75 | 0 | 27 | 37.17 | 0.75 | 0 | 0 | 0 | 7.6905369394 | 1.1398815626 | 3.02899397204007E-08 | 0.0062852534 | ENSSSCG00000013248 | NA |
3515807 | chr2 | 36259201 | 36259300 | 1 | 0 | 23 | 0 | 35.12 | 0 | 0.74 | 0 | 0 | 0 | 23 | 35.12 | 0.74 | -7.6060506188 | 0.9934313723 | 1.20863824109425E-07 | 0.0250796061 | NA | NA |
3640700 | chr2 | 48748501 | 48748600 | 4 | 0 | 24 | 0 | 36.65 | 0 | 0.66 | 0 | 0 | 0 | 24 | 36.65 | 0.66 | -7.6671425888 | 1.0466404624 | 6.05043434315258E-08 | 0.0125548328 | NA | NA |
3835270 | chr2 | 68205501 | 68205600 | 1 | 24 | 0 | 33.04 | 0 | 0.73 | 0 | 24 | 33.04 | 0.73 | 0 | 0 | 0 | 7.5214846498 | 0.9949480389 | 2.41450299325845E-07 | 0.0501016615 | NA | NA |
4070870 | chr2 | 91765501 | 91765600 | 2 | 26 | 0 | 35.79 | 0 | 0.72 | 0 | 26 | 35.79 | 0.72 | 0 | 0 | 0 | 7.6363577383 | 1.0931939799 | 6.05043434315258E-08 | 0.0125548328 | ENSSSCG00000014136 | NA |
5001207 | chr3 | 22229801 | 22229900 | 3 | 31 | 0 | 42.68 | 0 | 0.72 | 0 | 31 | 42.68 | 0.72 | 0 | 0 | 0 | 7.8889443296 | 1.3126573776 | 1.90354050254007E-09 | 0.0003949904 | ENSSSCG00000033674 | NA |
My query is -
1. How to analyse this result?
2. How to get exact position of chromosome ?
3. After annotation result show very less gene name , why ? and their is tow column in the end of table 1_id and 2_id , what these are ? is these column are result for sampleC and sample D ?
4. Can't understand the start and stop column information. any explanation? First row also shows some values what are these. ?
code ----
Set1 = MEDIPS.createSet(file = "SampleC_result.bam", BSgenome = BSgenome, extend = extend, shift = shift, uniq = uniq, window_size = ws)
Set2 = MEDIPS.createSet(file = "SampleD_result.bam", BSgenome = BSgenome, extend = extend, shift = shift, uniq = uniq, window_size = ws)
CS = MEDIPS.couplingVector(pattern = "CG", refObj = Set1)
#mr.edgeR = MEDIPS.meth(MSet1 = Set1, CSet = CS, p.adj = "bonferroni",diff.method = "edgeR", MeDIP = T, CNV = F, minRowSum = 10)
mr.edgeR_Set1 = MEDIPS.meth(MSet1 = Set1, CSet = CS, p.adj = "bonferroni",diff.method = "edgeR", MeDIP = T, CNV = F, minRowSum = 10)
mr.edgeR_both = MEDIPS.meth(MSet1 = Set1, MSet2 = Set2,CSet = CS, p.adj = "bonferroni",diff.method = "edgeR", MeDIP = T, CNV = F, minRowSum = 10)
View(mr.edgeR)
write.table(mr.edgeR, file="mredgeR_result.csv", row.names=FALSE, col.names=TRUE, sep='\t')
mr.edgeR.s = MEDIPS.selectSig(results = mr.edgeR, p.value = 0.1,adj = T, ratio = NULL, bg.counts = NULL, CNV = F)
ensembl = useDataset("sscrofa_gene_ensembl",mart=ensembl)
anno.mart.gene = MEDIPS.getAnnotation(dataset = c("sscrofa_gene_ensembl"),annotation = c("GENE"))
mr.edgeR.s.d = MEDIPS.setAnnotation(regions = mr.edgeR.s, annotation = anno.mart.gene)
write.table(mr.edgeR.s.d , file = "gene_ann_file.csv" ,row.names=FALSE, col.names=TRUE, sep='\t')
Thank you For reply ,
FOR QUESTION
2. How to get exact position of chromosome ?
Please see columns chr | start | stop.
Can you please elaborate this answer. because when i see the start and stop these showing some number with equal number of interval on the bases of window size (100). Actually i want exact position like chr1 - 1526 not range , is this possible ?
What is the significant of window size in MEDIPS ?