First Principal Component (PC1) Gene Signature

This helper function returns the first principal component from an assay stored as a matrix.

Usage

colPrinComp1(x, center = TRUE, scale = TRUE)

Arguments

x: (matrix)
containing numeric data with genes in rows and samples in columns, no missing values are allowed.
center: (flag)
whether the variables should be zero centered.
scale: (flag)
whether the variables should be scaled to have unit variance.

Value

A numeric vector containing the principal component values for each column in x.

Examples

object <- hermes_data %>%
  add_quality_flags() %>%
  filter() %>%
  normalize() %>%
  assay("counts")

colPrinComp1(object)
#> 06520011B0023R 06520067C0018R 06520063C0043R 06520105C0017R 06520092C0017R 
#>    -22.7211514    -16.5888471     -8.6643020    -20.3183592     13.4998779 
#> 06520103C0017R 06520001B0023R 06520022C0017R 06520062C0017R 06520101B0017R 
#>     17.9491775      4.7633163    -10.6928704    -16.1907212     30.3749930 
#> 06520047C0017R 06520024B0014R 06520080B0023R 06520093C0017R 06520070C0018R 
#>    -25.6029134    -18.1914202     -6.9932017     36.8659028      0.7099287 
#> 06520023C0018R 06520099B0017R 06520015C0016R 06520019C0023R 
#>     -5.3048871     32.7696234      9.9885728      4.3472814