Question: MEDIPS - Annotation output explanation
0
gravatar for vjain
17 months ago by
vjain0
vjain0 wrote:

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')

 

 

medips output • 307 views
ADD COMMENTlink modified 17 months ago • written 17 months ago by vjain0
Answer: MEDIPS - Annotation output explanation
0
gravatar for Lukas Chavez
17 months ago by
Lukas Chavez510
USA/La Jolla/UCSD
Lukas Chavez510 wrote:
Hi Vjain, My query is - 1. How to analyse this result? You table contains a list of potentially differentially enriched regions. What exactly this is and how you want to further analyze depends on your research question 2. How to get exact position of chromosome ? Please see columns chr | start | stop. 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 ? Not all DERs can be associated with a gene given the default parameters for the distance to a TSS in MEDIPS.getAnnotation. There are plenty of other tools available to annotate genomic regions in various ways. 4. Can't understand the start and stop column information. any explanation? First row also shows some values what are these. ? These are the genomic locations of a potential differentially enriched region (DER). First row is likely the row number (before extraction of significant windows). Hope that helps, Lukas On May 1, 2018, at 4:59 AM, vjain [bioc] <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> wrote: Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""/> User vjain<https: support.bioconductor.org="" u="" 15283=""/> wrote Question: MEDIPS - Annotation output explanation <https: support.bioconductor.org="" p="" 108407=""/> : 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') ________________________________ Post tags: MEDIPS, Output You may reply via email or visit MEDIPS - Annotation output explanation
ADD COMMENTlink written 17 months ago by Lukas Chavez510

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 ?

ADD REPLYlink written 17 months ago by vjain0
Answer: MEDIPS - Annotation output explanation
0
gravatar for vjain
17 months ago by
vjain0
vjain0 wrote:

Thank you For reply

ADD COMMENTlink modified 17 months ago • written 17 months ago by vjain0
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