artmsReplicatePlots {artMS} | R Documentation |
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
artmsReplicatePlots(input_file, keys_file, replicate_file, out_file, prot_exp = c("AB", "PH", "UB", "APMS"), verbose = TRUE)
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:
|
verbose |
(logical) |
The output file of the summary of features and intensity values
# 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'