dot-manageLibraryStrategy: Manage Library Strategy Formats

In ss-lab-cancerunit/SpiderSeqR: A Tool for Integration of Big Bio Data

Description

.manageLibraryStrategy by default converts between different formats of library strategy strings and offers a few other tasks related to library strategies

Usage

.manageLibraryStrategy(
  x,
  input,
  output,
  task = "conv",
  mismatch.ignore = FALSE
)

Arguments

x	Character vector to be converted
input	String denoting the input format (see below)
output	String denoting the output format (see below)
task	String denoting the task to be performed (see below)
mismatch.ignore	Logical denoting whether mismatches are allowed (if TRUE and no match, original character is returned)

Value

Library strategy in a desired format

Format types:

1. can (canonical) - as exists within the database

2. short (shorthand) - shortened version of the canonical form

3. syn (synonyms) - potential synonym

Available tasks:

1. conv - convert between formats

2. ex - produce a list of library strategies

3. check_can - check if x is in canonical form

Currently, the function supports the following conversions:

1. can -> short, i.e. input = "can", ouput = "short"

2. syn -> can, i.e. input = "syn", output = "can"

Examples

# Convert into short form
# .manageLibraryStrategy("RNA-Seq", input = "can", output = "short") 

# Convert into canonical form
# .manageLibraryStrategy("RNA", input = "syn", output = "can") 

# List supported formats for library strategy
# .manageLibraryStrategy(task = "ex") 

# Check whether library strategy is in canonical form
# .manageLibraryStrategy("RNA-Seq", task = "check_can") 

ss-lab-cancerunit/SpiderSeqR documentation built on Nov. 2, 2020, 12:18 a.m.