Calculate QC metrics

To calculate QC metrics such as standard deviation (sd), median absolute deviation (MAD), interquartile range (IQR), and Z score for read counts per condition/group of interest

Usage

compute_qc_metrics(data = NULL, group_by = NULL, order_by = NULL)

Arguments

data

A tidyseurat object merged with metadata. Must contain columns "Well_ID", "Row", "Column".

group_by

A metadata column name to group data

order_by

A column name or "median" for median of read counts.

Value

a list with a data frame with QC metrics and a box plot showing read counts per condition

Examples

data(mini_mac)
compute_qc_metrics(data = mini_mac, group_by = "combined_id", order_by = "median")

#> $stats_summary
#> # A tibble: 83 × 6
#>    combined_id     sd_value mad_value group_median z_score   IQR
#>    <chr>              <dbl>     <dbl>        <dbl>   <dbl> <dbl>
#>  1 Abemaciclib_0.1     39.1     32.6           465   0.542  38  
#>  2 Abemaciclib_1       32.5     47.4           415  -0.119  32.5
#>  3 Abemaciclib_10     104.      63.8           382  -0.555  99  
#>  4 Adavosertib_0.1     65.5     93.4           417  -0.093  65.5
#>  5 Adavosertib_1       63.1     83.0           440   0.212  63  
#>  6 Adavosertib_10      62.5     90.4           353  -0.939  62.5
#>  7 Anastrozole_0.1     13.2      7.41          466   0.555  12.5
#>  8 Anastrozole_1       50.7     13.3           405  -0.251  46  
#>  9 Anastrozole_10      24.3      2.96          491   0.886  21.5
#> 10 Azd.5991_0.1        66.6     53.4           425   0.013  64.5
#> # ℹ 73 more rows
#> 
#> $plot

#>