Differential Expression Analysis on Mzroll List

Differential Expression Analysis on Mzroll List

diffex_mzroll(
  mzroll_list,
  value_var,
  test_model,
  null_model = NULL,
  additional_grouping_vars = NULL,
  fdr_by_groupings = FALSE
)

Arguments

mzroll_list

output of process_mzroll or process_mzroll_multi

  • features: one row per unique analyte (defined by a unique groupId),

  • samples: one row per unique sample (defined by a unique sampleId),

  • measurements: one row per peak (samples x peakgroups)
value_var

measurement variable
test_model

a RHS formula for regression
null_model

if provided a null RHS formula to compare to test_model using the likelihood-ratio test.
additional_grouping_vars

sample-, or measurement-level variables to groupby when performing regression in addition to groupId.
fdr_by_groupings

if TRUE then calculate FDR separately across additional_grouping_vars (if they exist).

Value

a tibble of significance tests for each feature

Examples


# standard feature-wise regression
diffex_mzroll(
  nplug_mzroll_normalized,
  "normalized_log2_abundance",
  "limitation + limitation:DR + 0"
)

#> Warning: q-value calculation initially failed due to too many small p-values
#>         but claman was able to recover results
#> # A tibble: 1,060 × 8
#>    term     groupId estimate std.error statistic   p.value   qvalue diffex_label
#>    <chr>    <fct>      <dbl>     <dbl>     <dbl>     <dbl>    <dbl> <glue>      
#>  1 limitat… 1        0.423       0.303    1.40     1.82e-1  1.23e-1 1.396       
#>  2 limitat… 2       -1.44        0.115  -12.5      1.18e-9  6.07e-8 -12.467 *** 
#>  3 limitat… 3       -0.00625     0.397   -0.0158   9.88e-1  4.78e-1 -0.016      
#>  4 limitat… 4        0.744       0.622    1.20     2.49e-1  1.58e-1 1.196       
#>  5 limitat… 5        3.65        0.431    8.48     2.56e-7  1.73e-6 8.485 ***   
#>  6 limitat… 6        2.43        0.752    3.23     5.26e-3  6.13e-3 3.228 **    
#>  7 limitat… 7       -0.817       0.428   -1.91     7.40e-2  6.12e-2 -1.912 *    
#>  8 limitat… 8       -0.626       0.371   -1.69     1.11e-1  8.64e-2 -1.687 *    
#>  9 limitat… 9       -3.71        0.457   -8.11     4.64e-7  2.65e-6 -8.111 ***  
#> 10 limitat… 10      -0.655       0.300   -2.18     4.41e-2  4.05e-2 -2.185 *    
#> # … with 1,050 more rows

# separate regression for each feature and limitatioon
diffex_mzroll(
  nplug_mzroll_normalized,
  "normalized_log2_abundance",
  "DR + 0",
  additional_grouping_vars = "limitation"
)

#> # A tibble: 530 × 9
#>    term  groupId limitation estimate std.error statistic  p.value  qvalue
#>    <chr> <fct>   <chr>         <dbl>     <dbl>     <dbl>    <dbl>   <dbl>
#>  1 DR    1       NH4            6.80     0.580    11.7   0.000303 0.00643
#>  2 DR    1       URA            5.18     1.10      4.70  0.00929  0.0307 
#>  3 DR    1       PO4            2.32     5.29      0.438 0.679    0.346  
#>  4 DR    1       GLU            7.65     0.573    13.4   0.000182 0.00606
#>  5 DR    1       LEU            7.31     0.585    12.5   0.000236 0.00612
#>  6 DR    2       NH4           -6.95     1.71     -4.08  0.0151   0.0327 
#>  7 DR    2       URA           35.5      8.32      4.27  0.0129   0.0321 
#>  8 DR    2       PO4           -7.10     1.83     -3.88  0.0116   0.0311 
#>  9 DR    2       GLU           -6.48     1.67     -3.88  0.0179   0.0345 
#> 10 DR    2       LEU           -7.00     1.68     -4.16  0.0141   0.0327 
#> # … with 520 more rows, and 1 more variable: diffex_label <glue>

# feature-wise ANOVA
diffex_mzroll(
  nplug_mzroll_normalized,
  "normalized_log2_abundance",
  "limitation + 0",
  "0"
)

#> Warning: q-value calculation initially failed due to too many small p-values
#>         but claman was able to recover results
#> # A tibble: 106 × 10
#>    term  groupId res.df    rss    df  sumsq statistic  p.value   qvalue
#>    <chr> <fct>    <dbl>  <dbl> <dbl>  <dbl>     <dbl>    <dbl>    <dbl>
#>  1 LRT   1           21 31.1       5  30.8       4.16 8.75e- 3 1.31e- 3
#>  2 LRT   2           21  0.779     5 323.     1743.   9.56e-27 1.16e-25
#>  3 LRT   3           21 12.1       5   3.66      1.27 3.13e- 1 3.66e- 2
#>  4 LRT   4           21 11.0       5  27.3      10.4  3.99e- 5 1.31e- 5
#>  5 LRT   5           21 11.3       5 112.       41.5  3.48e-10 7.05e-10
#>  6 LRT   6           21 42.3       5  53.0       5.25 2.77e- 3 4.68e- 4
#>  7 LRT   7           21  5.23      5  14.5      11.6  1.77e- 5 6.14e- 6
#>  8 LRT   8           21  6.65      5  27.6      17.4  7.53e- 7 4.58e- 7
#>  9 LRT   9           21 21.5       5 148.       28.8  1.01e- 8 1.37e- 8
#> 10 LRT   10          21  2.35      5   1.53      2.72 4.77e- 2 6.30e- 3
#> # … with 96 more rows, and 1 more variable: diffex_label <glue>