Making Sincera object

[fereshtehizadi]

Sorry,

I now it is out of questioning but I am really interested in inferring GRN by Sincera on my single cell but whatever I am trying I am not able to make sc object. I read the vignette but I don't know how to replace my own expression data and cell information and make a new sc object. Please help me thank you

> sc <- construct(exprmatrix=my_matrix)
Error in construct(exprmatrix = my_matrix) : object 'rexpr' not found
> sc@rexprs=my_matrix
> sc <- construct(exprmatrix=rexprs)
Error in construct(exprmatrix = rexprs) : object 'rexprs' not found
>

[russHyde]

As I pointed out on biostars, the first error results from the construct function. When you call construct(exprmatrix=xxx) with neither a samplevector nor a samplefile argument, the construct code reaches a line that looks for rexpr in the namespace. This is a typo: it should be looking for rexprs. I'll submit a PR to fix that because you haven't.

I don't really understand the logic behind the other two lines you've written.

Seems the construct function was already flagged as a problem in #5

[fereshtehizadi]

Sorry, I am very new in git I did not what to do really

By changing rsampleinfo <- rep("sample1", dim(rexpr)[2]) to rsampleinfo <- rep("sample1", dim(rexprs)[2]) in source and running the source likely I construct my sincera object with my matrix

Sorry in gene information already you have 8 clusters and markers for each of them. I got confused if before clustering of your cells and obtaining markers for each cluster you have access to this information or this data frame would be produced after clustering and differential expression?? I mean this part

Please help me to be cleared

Thank you

> # gene information
> head(genes)
                          SYMBOL TF          TF_SOURCE use_as_marker_1 use_as_marker_2 use_as_marker_3 use_as_marker_5 use_as_marker_7 use_as_marker_8 use_as_marker_9
ENSMUSG00000044719 E230025N22Rik  0 genomatix_20140512               0               0               0               0               0               0               0
ENSMUSG00000044591    AC112933.1  0 genomatix_20140512               0               0               0               0               0               0               0
ENSMUSG00000044712       Slc38a6  0 genomatix_20140512               0               0               0               0               0               0               0
ENSMUSG00000044734     Serpinb1a  0 genomatix_20140512               0               0               0               0               0               0               0
ENSMUSG00000044726      BC030476  0 genomatix_20140512               0               0               0               0               0               0               0
ENSMUSG00000044724        Gpr152  0 genomatix_20140512               0               0               0               0               0               0               0
> 

[russHyde]

Hi again. I've submitted a patch to fix the problem. If it gets merged the constructor should work without having to specify either samplevector or samplefile. It's not my package, so I can't help with the detail of your example.

[fereshtehizadi]

Thank you for helping me