Regress out the effect of gene attributes

Source: R/regress_gene_info.R

Queries biomaRt for gene_attributes and then regresses them out of xmat.

regress_gene_info(xmat, attributes = c("size"), correction_method = "BH")

Arguments

xmat

gene x sample matrix.
attributes

Gene attributes to extract from biomaRt and then regress from xmat.
correction_method

Multiple-testing correction method to be passed to stats::p.adjust.

Examples

library(MAGMA.Celltyping)

#> Welcome to MAGMA.Celltyping.
#> This package depends on the use of the magma command line tool which is available from https://ctg.cncr.nl/software/magma.
#> Testing if you have it installed and available from the command line
#> 
#> Attaching package: 'MAGMA.Celltyping'
#> The following object is masked _by_ '.GlobalEnv':
#> 
#>     ctd_BlueLake2018_FrontalCortexOnly
#> The following objects are masked from 'package:phenomix':
#> 
#>     adjust_zstat, ctd_BlueLake2018_FrontalCortexOnly
xmat <- MAGMA.Celltyping::ctd_DRONC_human[[1]]$mean_exp[1:100, ]
adjusted_df <- regress_gene_info(xmat)

#> Error in regress_gene_info(xmat): could not find function "regress_gene_info"