confirmIntensityColumns: Identify the Intensity Columns

In ksong4/NetPhorce: Phosphoproteomics Network Analysis (NetPhorce)

Identify the Intensity Columns

Description

The function identifies the intensity columns. To correctly identify the columns and for downstream analysis the intensity column names should consist of a string of characters that includes the Condition, Time Point, and Replication or Independent experiment. These three variables need to be separated by an underscore, "_". The function takes as input CON, TIME, REP, separated by an underscore and in the order that these variables are found in the column names. For example, "CON_TIME_REP" will parse the intensity column named "Condition1_0minutes_1".

Usage

confirmIntensityColumns(
  rawMaxQuant = rawMaxQuant,
  intensityPattern = intensityPattern,
  filterCon = NULL,
  filterTime = NULL,
  filterRep = NULL,
  verbose = TRUE
)

Arguments

rawMaxQuant	(Required). Loaded raw MaxQuant data
intensityPattern	(Required). A string of CON, TIME, and REP separated by an underscore, "_". The condition term cannot start with a numeric value and the only acceptable symbols allowed in these three terms are Full-Stop/Period (.) or minus-dash (-). E.g. "CON_TIME_REP".
filterCon	(Optional). A list of conditions that you want to process. Only conditions from this list will be included in the downstream analyses.. E.g., c("Con1", "Con2)
filterTime	(Optional). A list of time points that you want to process. Only time points within this list will be included in the downstream analyses. E.g., c("0min", "5min", "15min")
filterRep	(Optional). A list of replications that you want to process. Only replications from this list will be included in the downstream analyses. E.g., c("R1", "R3", "R4")
verbose	(Optional). If TRUE, print a summary table of the intensity columns statistics for verification.

Value

list of data.frames

Examples

## Not run: 
## Loading One Condition Data
data("oneConditionExample")
## Identify the Intensity Columns and Condition, Time Point and Replication
intensityCols <- confirmIntensityColumns(rawMaxQuant = oneConditionExample,
                                     	intensityPattern = "con_time_rep",
                                     	verbose = TRUE)

## End(Not run)

ksong4/NetPhorce documentation built on March 24, 2023, 12:51 p.m.