correct_bias | R Documentation |
'correct_bias' is a wrapper function that computes and applies bias correction factors from extracted regression coefficients.
'correct_interxn' corrects RPF counts using bias correction factors generated from user-provided regression coefficients; this function will use regression coefficients corresponding to interaction terms.
'correct_marginal' corrects RPF counts using bias correction factors generated from user-provided regression coefficients; this function will ignore regression coefficients corresponding to interaction terms.
'correct_fixed' corrects RPF counts using user-specified values; this function is intended to be used with values from a simulation experiment.
'correct_gc' calculates a scaling factor for RPF GC content using user-provided regression coefficients and provide GC-corrected RPF counts.
correct_bias( dat, fit_coefs, f5_method = NULL, f3_method = NULL, correct_gc = T, which_column = "count" ) correct_interxn(dat, which_column, which_region, fit_coefs) correct_marginal(dat, which_column, which_region, fit_coefs) correct_fixed(dat, which_column, which_region, bias_params) correct_gc(dat, which_column, fit_coefs)
dat |
data frame containing regression predictors |
fit_coefs |
data frame; output from parse_coefs() |
f5_method |
character; name of function to apply for 5' correction |
f3_method |
character; name of function to apply for 3' correction |
correct_gc |
logical; whether to correct for RPF GC-content |
which_column |
character; name of column in dat containing uncorrected counts |
which_region |
character; one of "f5" or "f3" corresponding to RPF region |
bias_params |
named numeric vector; recovery probabilities from simulation |
A numeric vector corresponding to 'dat' containing bias-corrected RPF counts
correct_interxn
: Use regression coefficients as scaling factors for bias correction
correct_marginal
: Use regression coefficients as scaling factors for bias correction
correct_fixed
: Use simulation parameters as bias correction factors
correct_gc
: Correct for RPF GC-content
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