Thanks for developing such a nice package. I am testing it with your data and got an error message when I run the construct.high.res.reference function. The data structures of the input are:
str(coldata.df)
'data.frame': 12650 obs. of 5 variables:
$ tissue : chr "Pancreas" "Pancreas" "Pancreas" "Pancreas" ...
$ cell.type : chr "Stromal cell_Smoc2 high(Pancreas)" "Endothelial cell_Fabp4 high(Pancreas)" "Stromal cell_Smoc2 high(Pancreas)" "Stromal cell_Smoc2 high(Pancreas)" ...
$ cell.bc.tissue : chr "Pancreas" "Pancreas" "Pancreas" "Pancreas" ...
$ cell.type.1 : chr "Stromal cell_Smoc2 high" "Endothelial cell_Fabp4 high" "Stromal cell_Smoc2 high" "Stromal cell_Smoc2 high" ...
$ cell.type.alone: chr "Stromal cell" "Endothelial cell" "Stromal cell" "Stromal cell" ...
str(mca.counts.all.involved)
'data.frame': 20283 obs. of 8810 variables:
$ Pancreas_1.CGCTTGGTGGTATTTAGG: int 0 0 1 0 0 0 0 0 0 2 ...
$ Pancreas_1.CTCGCATACTTCGTATAC: int 0 0 1 0 0 0 0 0 0 0 ...
$ Pancreas_1.ACAATACCATCTACGAGC: int 0 0 0 0 1 0 0 0 0 0 ...
$ Pancreas_1.GAGGAGCACAAGCTCGCA: int 0 0 1 0 1 0 0 0 0 0 ...
$ Pancreas_1.CGCTTGTCGTAACATGAT: int 0 0 0 0 0 0 0 0 0 2 ...
$ Pancreas_1.TATGTACCTAGACGTGGC: int 0 0 0 2 0 0 0 0 0 0 ...
$ Pancreas_1.GCGAATCGCTTGACACCC: int 0 0 0 4 0 0 2 0 0 0 ...
$ Pancreas_1.GTCCCGCCGACGCTCCAT: int 0 0 0 0 0 1 0 0 0 3 ...
.....
ref.list <- construct.high.res.reference(mca.counts.all.involved, coldata.df = coldata.df, criteria = "cell.type.alone")
Error in norm.dt.st[, i] : subscript out of bounds
In addition: Warning messages:
1: In type.convert.default(X[[i]], ...) :
'as.is' should be specified by the caller; using TRUE
2: In type.convert.default(X[[i]], ...) :
'as.is' should be specified by the caller; using TRUE
3: In type.convert.default(X[[i]], ...) :
'as.is' should be specified by the caller; using TRUE
4: In type.convert.default(X[[i]], ...) :
'as.is' should be specified by the caller; using TRUE
Could you please let me know what is wrong? Thanks!
Thanks for developing such a nice package. I am testing it with your data and got an error message when I run the construct.high.res.reference function. The data structures of the input are:
ref.list <- construct.high.res.reference(mca.counts.all.involved, coldata.df = coldata.df, criteria = "cell.type.alone")
Error in norm.dt.st[, i] : subscript out of bounds
In addition: Warning messages:
1: In type.convert.default(X[[i]], ...) :
'as.is' should be specified by the caller; using TRUE
2: In type.convert.default(X[[i]], ...) :
'as.is' should be specified by the caller; using TRUE
3: In type.convert.default(X[[i]], ...) :
'as.is' should be specified by the caller; using TRUE
4: In type.convert.default(X[[i]], ...) :
'as.is' should be specified by the caller; using TRUE
Could you please let me know what is wrong? Thanks!