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Filter proteins by group level missing data

Source: R/filterProteins.R
filterbygroup_na.Rd

This function filters out proteins based on missing data at the group level.

Usage

filterbygroup_na(raw_df, set_na = 0.34, filter_condition = "either")

Arguments

raw_df

A raw_df object (output of create_df)

set_na

The proportion of missing data allowed. Default is 0.34 (one third of the samples in the group).

filter_condition

If set to "each", proteins that exceed the missing value proportion threshold set by set_na in each group will be removed (lenient). If set to "either"(default), proteins that exceed the missing value proportion threshold set by set_na in at least one group will be removed (stringent).

Value

A raw_df object.

Details

  • If filter_condition = "each", it then removes proteins (rows) from the data frame if the proportion of NAs in each group exceeds the threshold indicated by set_na (default is 0.34). This option is more lenient in comparison to filter_condition = "either", where proteins that exceeds the missing data threshold in either group gets removed from the data frame.

See also

create_df

Author

Chathurani Ranathunge

Examples

# \donttest{
# Generate a raw_df object with default settings. No technical replicates.
raw_df <- create_df(
prot_groups = "https://raw.githubusercontent.com/caranathunge/promor_example_data/main/pg1.txt",
exp_design = "https://raw.githubusercontent.com/caranathunge/promor_example_data/main/ed1.txt"
)
#> 0 empty row(s) removed.
#> 0 empty column(s) removed.
#> 80 protein(s) (rows) only identified by site removed.
#> 65 reverse protein(s) (rows) removed.
#> 42 protein potential contaminant(s) (rows) removed.
#> 1923 protein(s) identified by 2 or fewer unique peptides removed.
#> Zeros have been replaced with NAs.
#> Data have been log-transformed.

## Remove proteins that exceed 34% NAs in either group (default)
rawdf_filt1 <- filterbygroup_na(raw_df)
#> 224 proteins with higher than 34% NAs in at least one group removed.

## Remove proteins that exceed 34% NAs in each group
rawdf_filt2 <- filterbygroup_na(raw_df, filter_condition = "each")
#> 65 proteins with higher than 34% NAs in each group removed.

## Proportion of samples with NAs allowed in each group = 0.5
rawdf_filt3 <- filterbygroup_na(raw_df, set_na = 0.5, filter_condition = "each")
#> 65 proteins with higher than 50% NAs in each group removed.

# }