Extracting and replacing deep mutational scanning data

Source: R/deep_mutational_scan.R

Extracting and replacing data from deep_mutational_scan objects uses a mixture of list and data frame syntax. $ and [[ extract values from the main data fields (e.g. the gene or where the data is annotated) and [ provides a shortcut to access the main data table, which can otherwise be accessed via x$data.

# S3 method for deep_mutational_scan
[(x, i, j, drop = FALSE, ...)

# S3 method for deep_mutational_scan
[(x, i, j, ...) <- value

Arguments

x

deep_mutational_scan object.
i, j, ...

Indices to access.
drop

Coerce result to lowest possible dimension.
value

Value to set.

Functions

  • [.deep_mutational_scan: Extract

  • [<-.deep_mutational_scan: Assign

Examples

dms <- deepscanscape::deep_scans$p53

# Extract meta data:
dms$study

#> NULL
dms$impute_mask

#> NULL

dms[["gene"]]

#> NULL

# Replace meta data
dms$gene <- "new_gene"
dms$impute_mask <- NA

# Quickly access data columns:
dms["A"]

#> # A tibble: 191 x 1
#>          A
#>      <dbl>
#>  1 -0.772 
#>  2 -0.440 
#>  3 -0.695 
#>  4 -0.240 
#>  5 -0.778 
#>  6 -0.309 
#>  7 -0.544 
#>  8  0.154 
#>  9 -0.727 
#> 10  0.0170
#> # … with 181 more rows
dms[c(1,2,3), "C"]

#> # A tibble: 3 x 1
#>         C
#>     <dbl>
#> 1 -0.688 
#> 2 -0.722 
#> 3 -0.0939
dms[c("position", "wt", "A", "D")]

#> # A tibble: 191 x 4
#>    position wt          A       D
#>       <dbl> <chr>   <dbl>   <dbl>
#>  1        1 T     -0.772  -0.662 
#>  2        2 Y     -0.440  -0.879 
#>  3        3 Q     -0.695  -0.890 
#>  4        4 G     -0.240  -0.542 
#>  5        5 S     -0.778  -1.01  
#>  6        6 Y     -0.309   0.0561
#>  7        7 G     -0.544  -0.734 
#>  8        8 F      0.154   0.138 
#>  9        9 R     -0.727  -0.0746
#> 10       10 L      0.0170 -0.576 
#> # … with 181 more rows

# Quickly modify data columns
dms["position"] <- dms["position"] + 1