Subset DEXSeqDataSet In DEXSeq
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Entering edit mode
adelmane ▴ 20
@adelmane-9998
Last seen 8.2 years ago

Hello,

I'm new to RNAseq analysis, and would like to use DEXSeq for my project. For this experiment, I have 3 conditions, "Young", "Mid", and "Old". I used all 3 conditions to generate the DEXSeqDataSet and to estimate the dispersion estimates. I would now like to subset my DEXSeqDataSet to do comparisons like "Young vs. Old", and "Middle vs. Old". However, I haven't been successful in doing so. Do you have any suggestions for how to subset this object?

Current  colData:

> colData(my_dxd_disp)
DataFrame with 36 rows and 4 columns
      sample condition     exon sizeFactor
    <factor>  <factor> <factor>  <numeric>
1      A5619     Young     this   1.089542
2      A5036     Young     this   1.298421
3      S0539       Mid     this   1.208059
4      A5784       Mid     this   1.895919
5      H3592       Mid     this   1.633439
...      ...       ...      ...        ...
32    14-806       Old   others  0.7054832
33   15-1553       Old   others  0.9164503
34     A4891     Young   others  1.2563337
35     H1830       Mid   others  0.9854973
36     H1834       Mid   others  1.2850505

What I'd like to have for colData:

> colData(my_dxd_subsetted)
DataFrame with 22 rows and 4 columns
      sample condition     exon sizeFactor
    <factor>  <factor> <factor>  <numeric>
1      A5619     Young     this  1.0895423
2      A5036     Young     this  1.2984211
3    14-1240       Old     this  1.7338471
4     15-766       Old     this  1.3109882
5      S5005     Young     this  0.7085695
...      ...       ...      ...        ...
18    15-795       Old   others  0.8731101
19    16-041       Old   others  1.0258213
20    14-806       Old   others  0.7054832
21   15-1553       Old   others  0.9164503
22     A4891     Young   others  1.2563337

Thanks,

Emmalee

dexseq • 1.2k views
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Entering edit mode

Hi adelmane,

You could try:

my_dxd_disp <- my_dxd_disp[,colData(my_dxd_disp)$condition %in% c("Young", "Old")]

Alejandro

 

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Entering edit mode
adelmane ▴ 20
@adelmane-9998
Last seen 8.2 years ago

Thanks, that's perfect!

Emmalee

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