tidysc: Creates a 'tt' object from a 'tbl"

In stemangiola/ttSc: Friendly tidy wrappers for facilitating transcriptional analyses

Creates a 'tt' object from a 'tbl“

Description

tidysc_long() creates a 'tt' object from a 'tbl' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> |

tidysc_wide() creates a 'tt' object from a 'tbl' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> |

tidysc_cell_ranger() creates a 'tt' object from a 'tbl' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> |

Usage

tidysc_long(
  .data,
  .sample,
  .cell,
  .transcript,
  .abundance,
  species,
  min.transcripts = 400,
  min.cells = 5,
  ...
)

tidysc_wide(
  .data,
  .sample,
  .cell,
  .transcript_position,
  species,
  min.transcripts = 400,
  min.cells = 5,
  ...
)

tidysc_cell_ranger(
  dir_names,
  min.transcripts = 400,
  min.cells = 5,
  high.mito.thresh = 0.08,
  high.umi.thresh = 10000,
  species,
  genome = ifelse(species == "Human", "hg38", "mm10")
)

Arguments

.data	A 'tbl' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> |
.sample	The name of the sample column
.cell	The name of the cell column
.transcript	The name of the transcript/gene column
.abundance	The name of the transcript/gene abundance column

Details

\lifecycle

experimental

This function created a tidysc object and is useful if you want to avoid to specify .sample, .transcript and .abundance arguments all the times. The tidysc object have an attribute called parameters where these three arguments are stored as metadata. They can be extracted as attr(<object>, "parameters").

\lifecycle

experimental

This function created a tidysc object and is useful if you want to avoid to specify .sample, .transcript and .abundance arguments all the times. The tidysc object have an attribute called parameters where these three arguments are stored as metadata. They can be extracted as attr(<object>, "parameters").

\lifecycle

experimental

This function created a tidysc object and is useful if you want to avoid to specify .sample, .transcript and .abundance arguments all the times. The tidysc object have an attribute called parameters where these three arguments are stored as metadata. They can be extracted as attr(<object>, "parameters").

Value

A 'tidysc' object

A 'tidysc' object

A 'tidysc' object

Examples

my_tt =
    tidysc::counts %>%
    tidysc(sample, transcript, counts)

class(my_tt)







my_tt =
    tidysc::counts %>%
    tidysc(sample, transcript, counts)

class(my_tt)







my_tt =
    tidysc::counts %>%
    tidysc(sample, transcript, counts)

class(my_tt)

stemangiola/ttSc documentation built on Dec. 8, 2022, 2:37 a.m.