Using projectCellType_CP
Entering edit mode
2.2 years ago

I am trying to estimate the cell counts from given DNA methylation data and am using the FlowSorted.Blood.EPIC deconvolution library and when I try to estimate my cell counts with the function projectCellType_CP using this code:

est_cell_counts <-round(projectCellType_CP(beta_values_only_filtered[rownames(FlowSorted.Blood.EPIC),],
                                            FlowSorted.Blood.EPIC,lessThanOne =T)*100,2)

I get this error:

Error in `[.data.table`(beta_values_only_filtered, rownames(FlowSorted.Blood.EPIC),  : 
  When i is a data.table (or character vector), the columns to join by must be specified using 'on=' argument (see ?data.table), by keying x (i.e. sorted, and, marked as sorted, see ?setkey), or by sharing column names between x and i (i.e., a natural join). Keyed joins might have further speed benefits on very large data due to x being sorted in RAM.

How do I fix my code?

projectCellType_CP deconvolution cell • 450 views

Login before adding your answer.

Traffic: 1592 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6