make_outlier_table: Separate out the "i"th gene, take the bounds, and then create...

In ruggleslab/blacksheepr: Outlier Analysis for pairwise differential comparison

Separate out the "i"th gene, take the bounds, and then create a column that says whether or not this gene is high, low, or none in a sample with regards to the other samples in the dataset. Repeat this for every gene to create a reference table.

Description

Separate out the "i"th gene, take the bounds, and then create a column that says whether or not this gene is high, low, or none in a sample with regards to the other samples in the dataset. Repeat this for every gene to create a reference table.

Usage

make_outlier_table(intable, analyze_negative_outliers = FALSE)

Arguments

intable	table with all of the inputted information, samples along the x-axis, features along the y-axis
analyze_negative_outliers	DEFAULT: FALSE; Toggle the analysis of outliers in the negative direction. Will lead to the output of the outlier table containing "-1" values, in addition to negative outputs for boundaries and aggregate tables (if applicable)

Value

a list with varied sections depending on parameters: $outliertab - table converted to outlier form with 0s, 1s, and -1s, $upperboundtab - list of upper boundaries for outliers $lowerboundtab - list of lower boundaries of outliers $sampmedtab - list of median value per feature

Examples

data("sample_phosphodata")
reftable_function_out <- make_outlier_table(sample_phosphodata[1:1000,],
    analyze_negative_outliers = FALSE)
outliertab <- reftable_function_out$outliertab
upperboundtab <- reftable_function_out$upperboundtab
lowerboundtab <- reftable_function_out$lowerboundtab
sampmedtab <- reftable_function_out$sampmedtab

ruggleslab/blacksheepr documentation built on Feb. 27, 2023, 10:40 p.m.