| align_matrices | Align the rows and columns of two (or more) matrices |
| annotate.gct | Add annotations to a GCT object |
| annotate_gct | Add annotations to a GCT object |
| annotate_gct-method | Add annotations to a GCT object |
| cdesc_char | An example table of metadata, as would be parsed from or parse.gctx. Initially all the columns are of type character. |
| check_colnames | Check whether 'test_names' are columns in the 'data.frame' df |
| check_dups | Check for duplicates in a vector |
| distil | Collapse the rows or columns of a matrix using weighted averaging |
| ds | An example of a GCT object with row and column metadata and gene expression values in the matrix. |
| extract.gct | Exract elements from a GCT matrix |
| extract_gct | Exract elements from a GCT matrix |
| GCT | Initialize an object of class 'GCT' |
| GCT-class | An S4 class to represent a GCT object |
| gene_set | An example collection of gene sets as used in the Lamb 2006 CMap paper. |
| ids | Extract the or set row or column ids of a GCT object |
| ids-method | Extract the or set row or column ids of a GCT object |
| ids<- | Extract the or set row or column ids of a GCT object |
| ids<--method | Extract the or set row or column ids of a GCT object |
| is.wholenumber | Check if x is a whole number |
| kd_gct | An example GCT object of knockdown experiments targeting a subset of landmark genes. |
| lxb2mat | Read an LXB file and return a matrix |
| mat | Extract or set the matrix of GCT object |
| mat-method | Extract or set the matrix of GCT object |
| mat<- | Extract or set the matrix of GCT object |
| mat<--method | Extract or set the matrix of GCT object |
| melt.gct | Transform a GCT object in to a long form 'data.table' (aka 'melt') |
| melt_gct | Transform a GCT object in to a long form 'data.table' (aka 'melt') |
| melt_gct-method | Transform a GCT object in to a long form 'data.table' (aka 'melt') |
| merge.gct | Merge two GCT objects together |
| merge_gct | Merge two GCT objects together |
| merge_gct-method | Merge two GCT objects together |
| meta | Extract the or set metadata of a GCT object |
| meta-method | Extract the or set metadata of a GCT object |
| meta<- | Extract the or set metadata of a GCT object |
| meta<--method | Extract the or set metadata of a GCT object |
| na_pad_matrix | Pad a matrix with additional rows/columns of NA values |
| parse.gctx | Parse a GCTX file into the workspace as a GCT object |
| parse.gmt | Read a GMT file and return a list |
| parse.gmx | Read a GMX file and return a list |
| parse.grp | Read a GRP file and return a vector of its contents |
| parse_gctx | Parse a GCTX file into the workspace as a GCT object |
| parse_gmt | Read a GMT file and return a list |
| parse_gmx | Read a GMX file and return a list |
| parse_grp | Read a GRP file and return a vector of its contents |
| rank.gct | Convert a GCT object's matrix to ranks |
| rank_gct | Convert a GCT object's matrix to ranks |
| rank_gct-method | Convert a GCT object's matrix to ranks |
| read.gctx.ids | Read GCTX row or column ids |
| read.gctx.meta | Parse row or column metadata from GCTX files |
| read_gctx_ids | Read GCTX row or column ids |
| read_gctx_meta | Parse row or column metadata from GCTX files |
| robust_zscore | Compoute robust z-scores |
| subset.gct | Subset a gct object using the provided row and column ids |
| subset_gct | Subset a gct object using the provided row and column ids |
| subset_gct-method | Subset a gct object using the provided row and column ids |
| threshold | Threshold a numeric vector |
| transpose.gct | Transpose a GCT object |
| transpose_gct | Transpose a GCT object |
| transpose_gct-method | Transpose a GCT object |
| update.gctx | Update the matrix of an existing GCTX file |
| update_gctx | Update the matrix of an existing GCTX file |
| write.gct | Write a GCT object to disk in GCT format |
| write.gctx | Write a GCT object to disk in GCTX format |
| write.tbl | Write a 'data.frame' to a tab-delimited text file |
| write_gct | Write a GCT object to disk in GCT format |
| write_gctx | Write a GCT object to disk in GCTX format |
| write_gmt | Write a nested list to a GMT file |
| write_grp | Write a vector to a GRP file |
| write_tbl | Write a 'data.frame' to a tab-delimited text file |