artmsReplicatePlots {artMS}R Documentation

Create the replicate plots based on the pairings from the replicate plot file

Description

Outputs a replicate plots based on a user provied file containing the replicates to be compared. Values are based on the log2 value of the maximum intensities per modified sequence. The "replicate file" should describe which replicates of which conditions should be compared against each other. Each row represents a replicate plot to be created. The file should be structured using the following format and column names:

**condition1**|**rep1\_1**|**rep1\_2**|**condition2**|**rep2\_1**|**rep2\_2**
-----|-----|-----|-----|-----|-----
Cal33|Cal33-1|Cal33-2|HSC6|HSC6-1|HSC6-2
Cal33|Cal33-3|Cal33-4|HSC6|HSC6-3|HSC6-4

Usage

artmsReplicatePlots(input_file, keys_file, replicate_file, out_file,
  prot_exp = c("AB", "PH", "UB", "APMS"), verbose = TRUE)

Arguments

input_file

(char) MaxQuant evidence file and location

keys_file

(char) Keys file with the experimental details

replicate_file

(char) Replicate file. Check Vignette for examples

out_file

(char) Output .TEXT file with the intensity values of every feature

prot_exp

(char) Proteomics experiment. 4 options available:

  • AB: (default) protein abundance

  • APMS: affinity purification mass spectrometry

  • PH: protein phosphorylation

  • UB: protein ubiquitination (aka ubiquitylation)

verbose

(logical) TRUE (default) shows function messages

Value

The output file of the summary of features and intensity values

Examples

# First, let's make the "replicate file" (in a data.frame)
x_names <- c("condition1", "rep1_1", "rep1_2", "condition2", "rep2_1", 
"rep2_2")
x_values <- c("Cal33", "Cal33-1", "Cal33-4", "HSC6", "HSC6-2", "HSC6-3")
replica_info <- data.frame(t(x_values))
colnames(replica_info) <- x_names

# Now let's make the plots.
artmsReplicatePlots(input_file = artms_data_ph_evidence,
                     keys_file = artms_data_ph_keys,
                     replicate_file = replica_info,
                     out_file = NULL,
                     prot_exp = "PH")

# Remember that if you want to see the txt results and pdf file, just
# change out_file = NULL" to out_file = 'output_file.pdf'

[Package artMS version 1.0.12 Index]