I'm getting an error while trying to run the following command.
fitTimeSeries(CE_obj_file_aband_graph, lvl='Class', feature = "c__Clostridia",id="X.SampleID", time="Age", B=10, norm=F, log=F)
Error in sort.list(y) : 'x' must be atomic for 'sort.list'
Have you called 'sort' on a list?
Could someone tell me what is going wrong here? Output of str(pData(CE_obj_file_aband_graph)) is given below.
str(pData(CE_obj_file_aband_graph))
'data.frame': 104 obs. of 13 variables:
$ X.SampleID : Factor w/ 104 levels "C001","C002",..: 54 49 51 102 31 76 81 30 24 40 ...
$ BarcodeSequence : logi NA NA NA NA NA NA ...
$ LinkerPrimerSequence: logi NA NA NA NA NA NA ...
$ Age : num 1 16 16 16 8 5 5 5 5 8 ...
$ Tissue : Factor w/ 1 level "CE": 1 1 1 1 1 1 1 1 1 1 ...
$ Flock : Factor w/ 2 levels "R2 ","R3": 1 2 2 1 2 1 1 2 2 2 ...
$ AgeFlock : Factor w/ 12 levels "12Wk_R2","12Wk_R3",..: 5 4 4 3 12 9 9 10 10 12 ...
$ AgeTissue : Factor w/ 6 levels "12Wk_CE","16Wk_CE",..: 3 2 2 2 6 5 5 5 5 6 ...
$ AgeFlockTissue : Factor w/ 12 levels "12Wk_R2_CE","12Wk_R3_CE",..: 5 4 4 3 12 9 9 10 10 12 ...
$ Weight__g : int 153 14200 13400 16600 3500 1680 1418 1374 1663 3300 ...
$ AvgWt : int 143 13700 13700 16650 3270 1568 1568 1381 1381 3270 ...
$ Bird. : Factor w/ 104 levels "1","10","100",..: 13 8 10 5 78 48 54 66 59 88 ...
$ Description : Factor w/ 104 levels "C001","C002",..: 54 49 51 102 31 76 81 30 24 40 ...
I tried to build new MRexperiment object as described here:error using fitTimeSeries from metagenomeSeq. But still get the same error.
packageVersion('metagenomeSeq')
[1] ‘1.14.2’
Thanks
Thanks, Joseph!! That worked.